| 1 | ;;; GNU Guix --- Functional package management for GNU |
| 2 | ;;; Copyright © 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> |
| 3 | ;;; Copyright © 2016, 2017, 2018, 2020 Roel Janssen <roel@gnu.org> |
| 4 | ;;; Copyright © 2017, 2018, 2019 Tobias Geerinckx-Rice <me@tobias.gr> |
| 5 | ;;; Copyright © 2019 Simon Tournier <zimon.toutoune@gmail.com> |
| 6 | ;;; |
| 7 | ;;; This file is part of GNU Guix. |
| 8 | ;;; |
| 9 | ;;; GNU Guix is free software; you can redistribute it and/or modify it |
| 10 | ;;; under the terms of the GNU General Public License as published by |
| 11 | ;;; the Free Software Foundation; either version 3 of the License, or (at |
| 12 | ;;; your option) any later version. |
| 13 | ;;; |
| 14 | ;;; GNU Guix is distributed in the hope that it will be useful, but |
| 15 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of |
| 16 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 17 | ;;; GNU General Public License for more details. |
| 18 | ;;; |
| 19 | ;;; You should have received a copy of the GNU General Public License |
| 20 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. |
| 21 | |
| 22 | (define-module (gnu packages bioconductor) |
| 23 | #:use-module ((guix licenses) #:prefix license:) |
| 24 | #:use-module (guix packages) |
| 25 | #:use-module (guix download) |
| 26 | #:use-module (guix git-download) |
| 27 | #:use-module (guix build-system r) |
| 28 | #:use-module (gnu packages) |
| 29 | #:use-module (gnu packages base) |
| 30 | #:use-module (gnu packages bioinformatics) |
| 31 | #:use-module (gnu packages cran) |
| 32 | #:use-module (gnu packages compression) |
| 33 | #:use-module (gnu packages gcc) |
| 34 | #:use-module (gnu packages graph) |
| 35 | #:use-module (gnu packages graphviz) |
| 36 | #:use-module (gnu packages haskell-xyz) |
| 37 | #:use-module (gnu packages image) |
| 38 | #:use-module (gnu packages maths) |
| 39 | #:use-module (gnu packages netpbm) |
| 40 | #:use-module (gnu packages perl) |
| 41 | #:use-module (gnu packages pkg-config) |
| 42 | #:use-module (gnu packages statistics) |
| 43 | #:use-module (gnu packages web) |
| 44 | #:use-module (gnu packages xml) |
| 45 | #:use-module (srfi srfi-1)) |
| 46 | |
| 47 | \f |
| 48 | ;;; Annotations |
| 49 | |
| 50 | (define-public r-reactome-db |
| 51 | (package |
| 52 | (name "r-reactome-db") |
| 53 | (version "1.70.0") |
| 54 | (source |
| 55 | (origin |
| 56 | (method url-fetch) |
| 57 | (uri (bioconductor-uri "reactome.db" version 'annotation)) |
| 58 | (sha256 |
| 59 | (base32 |
| 60 | "05wc4fp0faq6h3kq5rwafnips043as31yq11mrjngfxvf5i10srg")))) |
| 61 | (properties `((upstream-name . "reactome.db"))) |
| 62 | (build-system r-build-system) |
| 63 | (propagated-inputs |
| 64 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 65 | (home-page "https://bioconductor.org/packages/reactome.db/") |
| 66 | (synopsis "Annotation maps for reactome") |
| 67 | (description |
| 68 | "This package provides a set of annotation maps for the REACTOME |
| 69 | database, assembled using data from REACTOME.") |
| 70 | (license license:cc-by4.0))) |
| 71 | |
| 72 | (define-public r-bsgenome-celegans-ucsc-ce6 |
| 73 | (package |
| 74 | (name "r-bsgenome-celegans-ucsc-ce6") |
| 75 | (version "1.4.0") |
| 76 | (source (origin |
| 77 | (method url-fetch) |
| 78 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce6" |
| 79 | version 'annotation)) |
| 80 | (sha256 |
| 81 | (base32 |
| 82 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) |
| 83 | (properties |
| 84 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) |
| 85 | (build-system r-build-system) |
| 86 | (propagated-inputs |
| 87 | `(("r-bsgenome" ,r-bsgenome))) |
| 88 | (home-page |
| 89 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") |
| 90 | (synopsis "Full genome sequences for Worm") |
| 91 | (description |
| 92 | "This package provides full genome sequences for Caenorhabditis |
| 93 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings |
| 94 | objects.") |
| 95 | (license license:artistic2.0))) |
| 96 | |
| 97 | (define-public r-bsgenome-celegans-ucsc-ce10 |
| 98 | (package |
| 99 | (name "r-bsgenome-celegans-ucsc-ce10") |
| 100 | (version "1.4.0") |
| 101 | (source (origin |
| 102 | (method url-fetch) |
| 103 | (uri (bioconductor-uri "BSgenome.Celegans.UCSC.ce10" |
| 104 | version 'annotation)) |
| 105 | (sha256 |
| 106 | (base32 |
| 107 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) |
| 108 | (properties |
| 109 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) |
| 110 | (build-system r-build-system) |
| 111 | (propagated-inputs |
| 112 | `(("r-bsgenome" ,r-bsgenome))) |
| 113 | (home-page |
| 114 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") |
| 115 | (synopsis "Full genome sequences for Worm") |
| 116 | (description |
| 117 | "This package provides full genome sequences for Caenorhabditis |
| 118 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings |
| 119 | objects.") |
| 120 | (license license:artistic2.0))) |
| 121 | |
| 122 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
| 123 | (package |
| 124 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") |
| 125 | (version "1.4.1") |
| 126 | (source (origin |
| 127 | (method url-fetch) |
| 128 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm6" |
| 129 | version 'annotation)) |
| 130 | (sha256 |
| 131 | (base32 |
| 132 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) |
| 133 | (properties |
| 134 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) |
| 135 | (build-system r-build-system) |
| 136 | (propagated-inputs |
| 137 | `(("r-bsgenome" ,r-bsgenome))) |
| 138 | (home-page |
| 139 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") |
| 140 | (synopsis "Full genome sequences for Fly") |
| 141 | (description |
| 142 | "This package provides full genome sequences for Drosophila |
| 143 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings |
| 144 | objects.") |
| 145 | (license license:artistic2.0))) |
| 146 | |
| 147 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
| 148 | (package |
| 149 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") |
| 150 | (version "1.4.0") |
| 151 | (source (origin |
| 152 | (method url-fetch) |
| 153 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3" |
| 154 | version 'annotation)) |
| 155 | (sha256 |
| 156 | (base32 |
| 157 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) |
| 158 | (properties |
| 159 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) |
| 160 | (build-system r-build-system) |
| 161 | (propagated-inputs |
| 162 | `(("r-bsgenome" ,r-bsgenome))) |
| 163 | (home-page |
| 164 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/") |
| 165 | (synopsis "Full genome sequences for Fly") |
| 166 | (description |
| 167 | "This package provides full genome sequences for Drosophila |
| 168 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in |
| 169 | Biostrings objects.") |
| 170 | (license license:artistic2.0))) |
| 171 | |
| 172 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
| 173 | (package |
| 174 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") |
| 175 | (version "1.3.99") |
| 176 | (source (origin |
| 177 | (method url-fetch) |
| 178 | (uri (bioconductor-uri "BSgenome.Dmelanogaster.UCSC.dm3.masked" |
| 179 | version 'annotation)) |
| 180 | (sha256 |
| 181 | (base32 |
| 182 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) |
| 183 | (properties |
| 184 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) |
| 185 | (build-system r-build-system) |
| 186 | (propagated-inputs |
| 187 | `(("r-bsgenome" ,r-bsgenome) |
| 188 | ("r-bsgenome-dmelanogaster-ucsc-dm3" |
| 189 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) |
| 190 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") |
| 191 | (synopsis "Full masked genome sequences for Fly") |
| 192 | (description |
| 193 | "This package provides full masked genome sequences for Drosophila |
| 194 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in |
| 195 | Biostrings objects. The sequences are the same as in |
| 196 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following |
| 197 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of |
| 198 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from |
| 199 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats |
| 200 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") |
| 201 | (license license:artistic2.0))) |
| 202 | |
| 203 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
| 204 | (package |
| 205 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") |
| 206 | (version "0.99.1") |
| 207 | (source (origin |
| 208 | (method url-fetch) |
| 209 | (uri (bioconductor-uri "BSgenome.Hsapiens.1000genomes.hs37d5" |
| 210 | version 'annotation)) |
| 211 | (sha256 |
| 212 | (base32 |
| 213 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) |
| 214 | (properties |
| 215 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) |
| 216 | (build-system r-build-system) |
| 217 | (propagated-inputs |
| 218 | `(("r-bsgenome" ,r-bsgenome))) |
| 219 | (home-page |
| 220 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") |
| 221 | (synopsis "Full genome sequences for Homo sapiens") |
| 222 | (description |
| 223 | "This package provides full genome sequences for Homo sapiens from |
| 224 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") |
| 225 | (license license:artistic2.0))) |
| 226 | |
| 227 | (define-public r-bsgenome-hsapiens-ncbi-grch38 |
| 228 | (package |
| 229 | (name "r-bsgenome-hsapiens-ncbi-grch38") |
| 230 | (version "1.3.1000") |
| 231 | (source |
| 232 | (origin |
| 233 | (method url-fetch) |
| 234 | (uri (bioconductor-uri "BSgenome.Hsapiens.NCBI.GRCh38" |
| 235 | version 'annotation)) |
| 236 | (sha256 |
| 237 | (base32 |
| 238 | "0y75qdq578fh6420vbvsbwmdw8jvr3g06qli2h3vj3pxmjykh9c1")))) |
| 239 | (properties `((upstream-name . "BSgenome.Hsapiens.NCBI.GRCh38"))) |
| 240 | (build-system r-build-system) |
| 241 | (propagated-inputs `(("r-bsgenome" ,r-bsgenome))) |
| 242 | (home-page |
| 243 | "https://bioconductor.org/packages/release/data/annotation/html/\ |
| 244 | BSgenome.Hsapiens.NCBI.GRCh38.html") |
| 245 | (synopsis "Full genome sequences for Homo sapiens (GRCh38)") |
| 246 | (description |
| 247 | "This package provides full genome sequences for Homo sapiens (Human) as |
| 248 | provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.") |
| 249 | (license license:artistic2.0))) |
| 250 | |
| 251 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
| 252 | (package |
| 253 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") |
| 254 | (version "1.3.99") |
| 255 | (source (origin |
| 256 | (method url-fetch) |
| 257 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19.masked" |
| 258 | version 'annotation)) |
| 259 | (sha256 |
| 260 | (base32 |
| 261 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) |
| 262 | (properties |
| 263 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) |
| 264 | (build-system r-build-system) |
| 265 | (propagated-inputs |
| 266 | `(("r-bsgenome" ,r-bsgenome) |
| 267 | ("r-bsgenome-hsapiens-ucsc-hg19" |
| 268 | ,r-bsgenome-hsapiens-ucsc-hg19))) |
| 269 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") |
| 270 | (synopsis "Full masked genome sequences for Homo sapiens") |
| 271 | (description |
| 272 | "This package provides full genome sequences for Homo sapiens (Human) as |
| 273 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The |
| 274 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of |
| 275 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS |
| 276 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of |
| 277 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem |
| 278 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by |
| 279 | default.") |
| 280 | (license license:artistic2.0))) |
| 281 | |
| 282 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
| 283 | (package |
| 284 | (name "r-bsgenome-mmusculus-ucsc-mm9") |
| 285 | (version "1.4.0") |
| 286 | (source (origin |
| 287 | (method url-fetch) |
| 288 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9" |
| 289 | version 'annotation)) |
| 290 | (sha256 |
| 291 | (base32 |
| 292 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) |
| 293 | (properties |
| 294 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) |
| 295 | (build-system r-build-system) |
| 296 | (propagated-inputs |
| 297 | `(("r-bsgenome" ,r-bsgenome))) |
| 298 | (home-page |
| 299 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") |
| 300 | (synopsis "Full genome sequences for Mouse") |
| 301 | (description |
| 302 | "This package provides full genome sequences for Mus musculus (Mouse) as |
| 303 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") |
| 304 | (license license:artistic2.0))) |
| 305 | |
| 306 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
| 307 | (package |
| 308 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") |
| 309 | (version "1.3.99") |
| 310 | (source (origin |
| 311 | (method url-fetch) |
| 312 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm9.masked" |
| 313 | version 'annotation)) |
| 314 | (sha256 |
| 315 | (base32 |
| 316 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) |
| 317 | (properties |
| 318 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) |
| 319 | (build-system r-build-system) |
| 320 | (propagated-inputs |
| 321 | `(("r-bsgenome" ,r-bsgenome) |
| 322 | ("r-bsgenome-mmusculus-ucsc-mm9" |
| 323 | ,r-bsgenome-mmusculus-ucsc-mm9))) |
| 324 | (home-page "https://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") |
| 325 | (synopsis "Full masked genome sequences for Mouse") |
| 326 | (description |
| 327 | "This package provides full genome sequences for Mus musculus (Mouse) as |
| 328 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The |
| 329 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of |
| 330 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS |
| 331 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of |
| 332 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem |
| 333 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by |
| 334 | default." ) |
| 335 | (license license:artistic2.0))) |
| 336 | |
| 337 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
| 338 | (package |
| 339 | (name "r-bsgenome-mmusculus-ucsc-mm10") |
| 340 | (version "1.4.0") |
| 341 | (source (origin |
| 342 | (method url-fetch) |
| 343 | (uri (bioconductor-uri "BSgenome.Mmusculus.UCSC.mm10" |
| 344 | version 'annotation)) |
| 345 | (sha256 |
| 346 | (base32 |
| 347 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) |
| 348 | (properties |
| 349 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) |
| 350 | (build-system r-build-system) |
| 351 | (propagated-inputs |
| 352 | `(("r-bsgenome" ,r-bsgenome))) |
| 353 | (home-page |
| 354 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") |
| 355 | (synopsis "Full genome sequences for Mouse") |
| 356 | (description |
| 357 | "This package provides full genome sequences for Mus |
| 358 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored |
| 359 | in Biostrings objects.") |
| 360 | (license license:artistic2.0))) |
| 361 | |
| 362 | (define-public r-org-ce-eg-db |
| 363 | (package |
| 364 | (name "r-org-ce-eg-db") |
| 365 | (version "3.7.0") |
| 366 | (source (origin |
| 367 | (method url-fetch) |
| 368 | (uri (bioconductor-uri "org.Ce.eg.db" version 'annotation)) |
| 369 | (sha256 |
| 370 | (base32 |
| 371 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) |
| 372 | (properties |
| 373 | `((upstream-name . "org.Ce.eg.db"))) |
| 374 | (build-system r-build-system) |
| 375 | (propagated-inputs |
| 376 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 377 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") |
| 378 | (synopsis "Genome wide annotation for Worm") |
| 379 | (description |
| 380 | "This package provides mappings from Entrez gene identifiers to various |
| 381 | annotations for the genome of the model worm Caenorhabditis elegans.") |
| 382 | (license license:artistic2.0))) |
| 383 | |
| 384 | (define-public r-org-dm-eg-db |
| 385 | (package |
| 386 | (name "r-org-dm-eg-db") |
| 387 | (version "3.7.0") |
| 388 | (source (origin |
| 389 | (method url-fetch) |
| 390 | (uri (bioconductor-uri "org.Dm.eg.db" version 'annotation)) |
| 391 | (sha256 |
| 392 | (base32 |
| 393 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) |
| 394 | (properties |
| 395 | `((upstream-name . "org.Dm.eg.db"))) |
| 396 | (build-system r-build-system) |
| 397 | (propagated-inputs |
| 398 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 399 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") |
| 400 | (synopsis "Genome wide annotation for Fly") |
| 401 | (description |
| 402 | "This package provides mappings from Entrez gene identifiers to various |
| 403 | annotations for the genome of the model fruit fly Drosophila melanogaster.") |
| 404 | (license license:artistic2.0))) |
| 405 | |
| 406 | (define-public r-org-dr-eg-db |
| 407 | (package |
| 408 | (name "r-org-dr-eg-db") |
| 409 | (version "3.7.0") |
| 410 | (source (origin |
| 411 | (method url-fetch) |
| 412 | (uri (bioconductor-uri "org.Dr.eg.db" version 'annotation)) |
| 413 | (sha256 |
| 414 | (base32 |
| 415 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) |
| 416 | (properties |
| 417 | `((upstream-name . "org.Dr.eg.db"))) |
| 418 | (build-system r-build-system) |
| 419 | (propagated-inputs |
| 420 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 421 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") |
| 422 | (synopsis "Annotation for Zebrafish") |
| 423 | (description |
| 424 | "This package provides genome wide annotations for Zebrafish, primarily |
| 425 | based on mapping using Entrez Gene identifiers.") |
| 426 | (license license:artistic2.0))) |
| 427 | |
| 428 | (define-public r-org-hs-eg-db |
| 429 | (package |
| 430 | (name "r-org-hs-eg-db") |
| 431 | (version "3.7.0") |
| 432 | (source (origin |
| 433 | (method url-fetch) |
| 434 | (uri (bioconductor-uri "org.Hs.eg.db" version 'annotation)) |
| 435 | (sha256 |
| 436 | (base32 |
| 437 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) |
| 438 | (properties |
| 439 | `((upstream-name . "org.Hs.eg.db"))) |
| 440 | (build-system r-build-system) |
| 441 | (propagated-inputs |
| 442 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 443 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") |
| 444 | (synopsis "Genome wide annotation for Human") |
| 445 | (description |
| 446 | "This package contains genome-wide annotations for Human, primarily based |
| 447 | on mapping using Entrez Gene identifiers.") |
| 448 | (license license:artistic2.0))) |
| 449 | |
| 450 | (define-public r-org-mm-eg-db |
| 451 | (package |
| 452 | (name "r-org-mm-eg-db") |
| 453 | (version "3.7.0") |
| 454 | (source (origin |
| 455 | (method url-fetch) |
| 456 | (uri (bioconductor-uri "org.Mm.eg.db" version 'annotation)) |
| 457 | (sha256 |
| 458 | (base32 |
| 459 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) |
| 460 | (properties |
| 461 | `((upstream-name . "org.Mm.eg.db"))) |
| 462 | (build-system r-build-system) |
| 463 | (propagated-inputs |
| 464 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 465 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") |
| 466 | (synopsis "Genome wide annotation for Mouse") |
| 467 | (description |
| 468 | "This package provides mappings from Entrez gene identifiers to various |
| 469 | annotations for the genome of the model mouse Mus musculus.") |
| 470 | (license license:artistic2.0))) |
| 471 | |
| 472 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
| 473 | (package |
| 474 | (name "r-bsgenome-hsapiens-ucsc-hg19") |
| 475 | (version "1.4.0") |
| 476 | (source (origin |
| 477 | (method url-fetch) |
| 478 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg19" |
| 479 | version 'annotation)) |
| 480 | (sha256 |
| 481 | (base32 |
| 482 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) |
| 483 | (properties |
| 484 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) |
| 485 | (build-system r-build-system) |
| 486 | (propagated-inputs |
| 487 | `(("r-bsgenome" ,r-bsgenome))) |
| 488 | (home-page |
| 489 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") |
| 490 | (synopsis "Full genome sequences for Homo sapiens") |
| 491 | (description |
| 492 | "This package provides full genome sequences for Homo sapiens as provided |
| 493 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") |
| 494 | (license license:artistic2.0))) |
| 495 | |
| 496 | (define-public r-bsgenome-hsapiens-ucsc-hg38 |
| 497 | (package |
| 498 | (name "r-bsgenome-hsapiens-ucsc-hg38") |
| 499 | (version "1.4.1") |
| 500 | (source (origin |
| 501 | (method url-fetch) |
| 502 | (uri (bioconductor-uri "BSgenome.Hsapiens.UCSC.hg38" |
| 503 | version 'annotation)) |
| 504 | (sha256 |
| 505 | (base32 |
| 506 | "1ql08pvi4vv0ynvg4qs9kysw1c7s3crkgin6zxvgzqk6fray9mvi")))) |
| 507 | (properties |
| 508 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg38"))) |
| 509 | (build-system r-build-system) |
| 510 | (propagated-inputs |
| 511 | `(("r-bsgenome" ,r-bsgenome))) |
| 512 | (home-page |
| 513 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg38/") |
| 514 | (synopsis "Full genome sequences for Homo sapiens") |
| 515 | (description |
| 516 | "This package provides full genome sequences for Homo sapiens (Human) |
| 517 | as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.") |
| 518 | (license license:artistic2.0))) |
| 519 | |
| 520 | (define-public r-ensdb-hsapiens-v75 |
| 521 | (package |
| 522 | (name "r-ensdb-hsapiens-v75") |
| 523 | (version "2.99.0") |
| 524 | (source |
| 525 | (origin |
| 526 | (method url-fetch) |
| 527 | (uri (bioconductor-uri "EnsDb.Hsapiens.v75" version 'annotation)) |
| 528 | (sha256 |
| 529 | (base32 |
| 530 | "0jx6rf6v0j8yr07q3c1h7s121901dc400nm6xaiv4i7kb5czjn9c")))) |
| 531 | (properties |
| 532 | `((upstream-name . "EnsDb.Hsapiens.v75"))) |
| 533 | (build-system r-build-system) |
| 534 | (propagated-inputs |
| 535 | `(("r-ensembldb" ,r-ensembldb))) |
| 536 | (home-page "https://bioconductor.org/packages/EnsDb.Hsapiens.v75") |
| 537 | (synopsis "Ensembl based annotation package") |
| 538 | (description |
| 539 | "This package exposes an annotation database generated from Ensembl.") |
| 540 | (license license:artistic2.0))) |
| 541 | |
| 542 | (define-public r-genelendatabase |
| 543 | (package |
| 544 | (name "r-genelendatabase") |
| 545 | (version "1.18.0") |
| 546 | (source |
| 547 | (origin |
| 548 | (method url-fetch) |
| 549 | (uri (bioconductor-uri "geneLenDataBase" version 'experiment)) |
| 550 | (sha256 |
| 551 | (base32 |
| 552 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
| 553 | (properties |
| 554 | `((upstream-name . "geneLenDataBase"))) |
| 555 | (build-system r-build-system) |
| 556 | (propagated-inputs |
| 557 | `(("r-rtracklayer" ,r-rtracklayer) |
| 558 | ("r-genomicfeatures" ,r-genomicfeatures))) |
| 559 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") |
| 560 | (synopsis "Lengths of mRNA transcripts for a number of genomes") |
| 561 | (description |
| 562 | "This package provides the lengths of mRNA transcripts for a number of |
| 563 | genomes and gene ID formats, largely based on the UCSC table browser.") |
| 564 | (license license:lgpl2.0+))) |
| 565 | |
| 566 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
| 567 | (package |
| 568 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") |
| 569 | (version "3.2.2") |
| 570 | (source (origin |
| 571 | (method url-fetch) |
| 572 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg19.knownGene" |
| 573 | version 'annotation)) |
| 574 | (sha256 |
| 575 | (base32 |
| 576 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) |
| 577 | (properties |
| 578 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) |
| 579 | (build-system r-build-system) |
| 580 | (propagated-inputs |
| 581 | `(("r-genomicfeatures" ,r-genomicfeatures))) |
| 582 | (home-page |
| 583 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") |
| 584 | (synopsis "Annotation package for human genome in TxDb format") |
| 585 | (description |
| 586 | "This package provides an annotation database of Homo sapiens genome |
| 587 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" |
| 588 | track. The database is exposed as a @code{TxDb} object.") |
| 589 | (license license:artistic2.0))) |
| 590 | |
| 591 | (define-public r-txdb-hsapiens-ucsc-hg38-knowngene |
| 592 | (package |
| 593 | (name "r-txdb-hsapiens-ucsc-hg38-knowngene") |
| 594 | (version "3.4.6") |
| 595 | (source (origin |
| 596 | (method url-fetch) |
| 597 | (uri (bioconductor-uri "TxDb.Hsapiens.UCSC.hg38.knownGene" |
| 598 | version 'annotation)) |
| 599 | (sha256 |
| 600 | (base32 |
| 601 | "12j7rri9r129v9w1yiqadg952dx462dh092sxif3r5kk8l7bxkn9")))) |
| 602 | (properties |
| 603 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg38.knownGene"))) |
| 604 | (build-system r-build-system) |
| 605 | (propagated-inputs |
| 606 | `(("r-genomicfeatures" ,r-genomicfeatures))) |
| 607 | (home-page |
| 608 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg38.knownGene/") |
| 609 | (synopsis "Annotation package for human genome in TxDb format") |
| 610 | (description |
| 611 | "This package provides an annotation database of Homo sapiens genome |
| 612 | data. It is derived from the UCSC hg38 genome and based on the \"knownGene\" |
| 613 | track. The database is exposed as a @code{TxDb} object.") |
| 614 | (license license:artistic2.0))) |
| 615 | |
| 616 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
| 617 | (package |
| 618 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") |
| 619 | (version "3.2.2") |
| 620 | (source (origin |
| 621 | (method url-fetch) |
| 622 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm9.knownGene" |
| 623 | version 'annotation)) |
| 624 | (sha256 |
| 625 | (base32 |
| 626 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) |
| 627 | (properties |
| 628 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) |
| 629 | (build-system r-build-system) |
| 630 | (propagated-inputs |
| 631 | `(("r-genomicfeatures" ,r-genomicfeatures) |
| 632 | ("r-annotationdbi" ,r-annotationdbi))) |
| 633 | (home-page |
| 634 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") |
| 635 | (synopsis "Annotation package for mouse genome in TxDb format") |
| 636 | (description |
| 637 | "This package provides an annotation database of Mouse genome data. It |
| 638 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The |
| 639 | database is exposed as a @code{TxDb} object.") |
| 640 | (license license:artistic2.0))) |
| 641 | |
| 642 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
| 643 | (package |
| 644 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") |
| 645 | (version "3.10.0") |
| 646 | (source (origin |
| 647 | (method url-fetch) |
| 648 | (uri (bioconductor-uri "TxDb.Mmusculus.UCSC.mm10.knownGene" |
| 649 | version 'annotation)) |
| 650 | (sha256 |
| 651 | (base32 |
| 652 | "0xs9npnhbwll7p62hibs02y4ac23jchdcr25i6a7qwq1kms82qk9")))) |
| 653 | (properties |
| 654 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) |
| 655 | (build-system r-build-system) |
| 656 | (propagated-inputs |
| 657 | `(("r-bsgenome" ,r-bsgenome) |
| 658 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 659 | ("r-annotationdbi" ,r-annotationdbi))) |
| 660 | (home-page |
| 661 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") |
| 662 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") |
| 663 | (description |
| 664 | "This package loads a TxDb object, which is an R interface to |
| 665 | prefabricated databases contained in this package. This package provides |
| 666 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) |
| 667 | based on the knownGene track.") |
| 668 | (license license:artistic2.0))) |
| 669 | |
| 670 | (define-public r-txdb-celegans-ucsc-ce6-ensgene |
| 671 | (package |
| 672 | (name "r-txdb-celegans-ucsc-ce6-ensgene") |
| 673 | (version "3.2.2") |
| 674 | (source |
| 675 | (origin |
| 676 | (method url-fetch) |
| 677 | (uri (bioconductor-uri "TxDb.Celegans.UCSC.ce6.ensGene" |
| 678 | version 'annotation)) |
| 679 | (sha256 |
| 680 | (base32 |
| 681 | "1sgppva33cdy4isj2is8mfalj5gmmkpbkq9w1d83a4agcq31mi90")))) |
| 682 | (properties |
| 683 | `((upstream-name . "TxDb.Celegans.UCSC.ce6.ensGene"))) |
| 684 | (build-system r-build-system) |
| 685 | (propagated-inputs |
| 686 | `(("r-annotationdbi" ,r-annotationdbi) |
| 687 | ("r-genomicfeatures" ,r-genomicfeatures))) |
| 688 | (home-page "https://bioconductor.org/packages/TxDb.Celegans.UCSC.ce6.ensGene/") |
| 689 | (synopsis "Annotation package for C elegans TxDb objects") |
| 690 | (description |
| 691 | "This package exposes a C elegans annotation database generated from UCSC |
| 692 | by exposing these as TxDb objects.") |
| 693 | (license license:artistic2.0))) |
| 694 | |
| 695 | (define-public r-fdb-infiniummethylation-hg19 |
| 696 | (package |
| 697 | (name "r-fdb-infiniummethylation-hg19") |
| 698 | (version "2.2.0") |
| 699 | (source (origin |
| 700 | (method url-fetch) |
| 701 | (uri (bioconductor-uri "FDb.InfiniumMethylation.hg19" |
| 702 | version 'annotation)) |
| 703 | (sha256 |
| 704 | (base32 |
| 705 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) |
| 706 | (properties |
| 707 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) |
| 708 | (build-system r-build-system) |
| 709 | (propagated-inputs |
| 710 | `(("r-biostrings" ,r-biostrings) |
| 711 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 712 | ("r-annotationdbi" ,r-annotationdbi) |
| 713 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) |
| 714 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) |
| 715 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") |
| 716 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") |
| 717 | (description |
| 718 | "This is an annotation package for Illumina Infinium DNA methylation |
| 719 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 |
| 720 | annotations.") |
| 721 | (license license:artistic2.0))) |
| 722 | |
| 723 | (define-public r-illuminahumanmethylationepicmanifest |
| 724 | (package |
| 725 | (name "r-illuminahumanmethylationepicmanifest") |
| 726 | (version "0.3.0") |
| 727 | (source (origin |
| 728 | (method url-fetch) |
| 729 | (uri (bioconductor-uri "IlluminaHumanMethylationEPICmanifest" |
| 730 | version 'annotation)) |
| 731 | (sha256 |
| 732 | (base32 |
| 733 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) |
| 734 | (properties |
| 735 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) |
| 736 | (build-system r-build-system) |
| 737 | (propagated-inputs |
| 738 | `(("r-minfi" ,r-minfi))) |
| 739 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") |
| 740 | (synopsis "Manifest for Illumina's EPIC methylation arrays") |
| 741 | (description |
| 742 | "This is a manifest package for Illumina's EPIC methylation arrays.") |
| 743 | (license license:artistic2.0))) |
| 744 | |
| 745 | (define-public r-ideoviz |
| 746 | (package |
| 747 | (name "r-ideoviz") |
| 748 | (version "1.24.0") |
| 749 | (source (origin |
| 750 | (method url-fetch) |
| 751 | (uri (bioconductor-uri "IdeoViz" version)) |
| 752 | (sha256 |
| 753 | (base32 |
| 754 | "1ndj14qhpgidjb4qsga80ghqzz1x8kvy2gy1bvvgwlkfxa62rn50")))) |
| 755 | (build-system r-build-system) |
| 756 | (propagated-inputs |
| 757 | `(("r-biobase" ,r-biobase) |
| 758 | ("r-iranges" ,r-iranges) |
| 759 | ("r-genomicranges" ,r-genomicranges) |
| 760 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 761 | ("r-rtracklayer" ,r-rtracklayer) |
| 762 | ("r-genomeinfodb" ,r-genomeinfodb))) |
| 763 | (home-page "https://bioconductor.org/packages/IdeoViz/") |
| 764 | (synopsis "Plots data along a chromosomal ideogram") |
| 765 | (description "This package provides functions to plot data associated with |
| 766 | arbitrary genomic intervals along chromosomal ideogram.") |
| 767 | (license license:gpl2))) |
| 768 | |
| 769 | ;; This is a CRAN package, but it depends on r-bsgenome-hsapiens-ucsc-hg19 |
| 770 | ;; from Bioconductor. |
| 771 | (define-public r-deconstructsigs |
| 772 | (package |
| 773 | (name "r-deconstructsigs") |
| 774 | (version "1.8.0") |
| 775 | (source (origin |
| 776 | (method url-fetch) |
| 777 | (uri (cran-uri "deconstructSigs" version)) |
| 778 | (sha256 |
| 779 | (base32 |
| 780 | "014x0nb23jb98666kaav2phkvmkr38pi38jv0dqd4jv7zp0gdf1a")))) |
| 781 | (properties |
| 782 | `((upstream-name . "deconstructSigs"))) |
| 783 | (build-system r-build-system) |
| 784 | (propagated-inputs |
| 785 | `(("r-bsgenome" ,r-bsgenome) |
| 786 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 787 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 788 | ("r-reshape2" ,r-reshape2))) |
| 789 | (home-page "https://github.com/raerose01/deconstructSigs") |
| 790 | (synopsis "Identifies signatures present in a tumor sample") |
| 791 | (description "This package takes sample information in the form of the |
| 792 | fraction of mutations in each of 96 trinucleotide contexts and identifies |
| 793 | the weighted combination of published signatures that, when summed, most |
| 794 | closely reconstructs the mutational profile.") |
| 795 | (license license:gpl2+))) |
| 796 | |
| 797 | ;; This is a CRAN package, but it depends on Bioconductor packages. |
| 798 | (define-public r-nmf |
| 799 | (package |
| 800 | (name "r-nmf") |
| 801 | (version "0.22.0") |
| 802 | (source |
| 803 | (origin |
| 804 | (method url-fetch) |
| 805 | (uri (cran-uri "NMF" version)) |
| 806 | (sha256 |
| 807 | (base32 |
| 808 | "0b2ls3x1nkrnam45hagpys624nzxj3v7kxnp0q216yakvx5h57cq")))) |
| 809 | (properties `((upstream-name . "NMF"))) |
| 810 | (build-system r-build-system) |
| 811 | (propagated-inputs |
| 812 | `(("r-cluster" ,r-cluster) |
| 813 | ("r-biobase" ,r-biobase) |
| 814 | ("r-biocmanager" ,r-biocmanager) |
| 815 | ("r-bigmemory" ,r-bigmemory) ; suggested |
| 816 | ("r-synchronicity" ,r-synchronicity) ; suggested |
| 817 | ("r-colorspace" ,r-colorspace) |
| 818 | ("r-digest" ,r-digest) |
| 819 | ("r-doparallel" ,r-doparallel) |
| 820 | ("r-foreach" ,r-foreach) |
| 821 | ("r-ggplot2" ,r-ggplot2) |
| 822 | ("r-gridbase" ,r-gridbase) |
| 823 | ("r-pkgmaker" ,r-pkgmaker) |
| 824 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 825 | ("r-registry" ,r-registry) |
| 826 | ("r-reshape2" ,r-reshape2) |
| 827 | ("r-rngtools" ,r-rngtools) |
| 828 | ("r-stringr" ,r-stringr))) |
| 829 | (home-page "http://renozao.github.io/NMF") |
| 830 | (synopsis "Algorithms and framework for nonnegative matrix factorization") |
| 831 | (description |
| 832 | "This package provides a framework to perform Non-negative Matrix |
| 833 | Factorization (NMF). The package implements a set of already published |
| 834 | algorithms and seeding methods, and provides a framework to test, develop and |
| 835 | plug new or custom algorithms. Most of the built-in algorithms have been |
| 836 | optimized in C++, and the main interface function provides an easy way of |
| 837 | performing parallel computations on multicore machines.") |
| 838 | (license license:gpl2+))) |
| 839 | |
| 840 | (define-public r-do-db |
| 841 | (package |
| 842 | (name "r-do-db") |
| 843 | (version "2.9") |
| 844 | (source (origin |
| 845 | (method url-fetch) |
| 846 | (uri (bioconductor-uri "DO.db" version 'annotation)) |
| 847 | (sha256 |
| 848 | (base32 |
| 849 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) |
| 850 | (properties |
| 851 | `((upstream-name . "DO.db"))) |
| 852 | (build-system r-build-system) |
| 853 | (propagated-inputs |
| 854 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 855 | (home-page "https://www.bioconductor.org/packages/DO.db/") |
| 856 | (synopsis "Annotation maps describing the entire Disease Ontology") |
| 857 | (description |
| 858 | "This package provides a set of annotation maps describing the entire |
| 859 | Disease Ontology.") |
| 860 | (license license:artistic2.0))) |
| 861 | |
| 862 | (define-public r-pasilla |
| 863 | (package |
| 864 | (name "r-pasilla") |
| 865 | (version "1.14.0") |
| 866 | (source (origin |
| 867 | (method url-fetch) |
| 868 | (uri (string-append |
| 869 | "http://bioconductor.org/packages/release/data/experiment" |
| 870 | "/src/contrib/pasilla_" version ".tar.gz")) |
| 871 | (sha256 |
| 872 | (base32 |
| 873 | "0h124i2fb2lbj2k48zzf1n7ldqa471bs26fbd9vw50299aqx28x0")))) |
| 874 | (build-system r-build-system) |
| 875 | (propagated-inputs |
| 876 | `(("r-biocstyle" ,r-biocstyle) |
| 877 | ("r-dexseq" ,r-dexseq) |
| 878 | ("r-knitr" ,r-knitr) |
| 879 | ("r-rmarkdown" ,r-rmarkdown))) |
| 880 | (home-page "https://www.bioconductor.org/packages/pasilla/") |
| 881 | (synopsis "Data package with per-exon and per-gene read counts") |
| 882 | (description "This package provides per-exon and per-gene read counts |
| 883 | computed for selected genes from RNA-seq data that were presented in the |
| 884 | article 'Conservation of an RNA regulatory map between Drosophila and mammals' |
| 885 | by Brooks et al., Genome Research 2011.") |
| 886 | (license license:lgpl2.1+))) |
| 887 | |
| 888 | (define-public r-pfam-db |
| 889 | (package |
| 890 | (name "r-pfam-db") |
| 891 | (version "3.8.2") |
| 892 | (source |
| 893 | (origin |
| 894 | (method url-fetch) |
| 895 | (uri (bioconductor-uri "PFAM.db" version 'annotation)) |
| 896 | (sha256 |
| 897 | (base32 |
| 898 | "0rn1arzzcniy3yyc4yc44vn40g0cqss37dhwnvsgxpfayqq1k59s")))) |
| 899 | (properties `((upstream-name . "PFAM.db"))) |
| 900 | (build-system r-build-system) |
| 901 | (propagated-inputs |
| 902 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 903 | (home-page "https://bioconductor.org/packages/PFAM.db") |
| 904 | (synopsis "Set of protein ID mappings for PFAM") |
| 905 | (description |
| 906 | "This package provides a set of protein ID mappings for PFAM, assembled |
| 907 | using data from public repositories.") |
| 908 | (license license:artistic2.0))) |
| 909 | |
| 910 | (define-public r-phastcons100way-ucsc-hg19 |
| 911 | (package |
| 912 | (name "r-phastcons100way-ucsc-hg19") |
| 913 | (version "3.7.2") |
| 914 | (source |
| 915 | (origin |
| 916 | (method url-fetch) |
| 917 | (uri (bioconductor-uri "phastCons100way.UCSC.hg19" |
| 918 | version 'annotation)) |
| 919 | (sha256 |
| 920 | (base32 |
| 921 | "1jmc4k4zgkx5vr2plnidnd9bidlwlb0kr7mjg60cqjw7dq7jl1fa")))) |
| 922 | (properties |
| 923 | `((upstream-name . "phastCons100way.UCSC.hg19"))) |
| 924 | (build-system r-build-system) |
| 925 | (propagated-inputs |
| 926 | `(("r-bsgenome" ,r-bsgenome) |
| 927 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 928 | ("r-genomicranges" ,r-genomicranges) |
| 929 | ("r-genomicscores" ,r-genomicscores) |
| 930 | ("r-iranges" ,r-iranges) |
| 931 | ("r-s4vectors" ,r-s4vectors))) |
| 932 | (home-page "https://bioconductor.org/packages/phastCons100way.UCSC.hg19") |
| 933 | (synopsis "UCSC phastCons conservation scores for hg19") |
| 934 | (description |
| 935 | "This package provides UCSC phastCons conservation scores for the human |
| 936 | genome (hg19) calculated from multiple alignments with other 99 vertebrate |
| 937 | species.") |
| 938 | (license license:artistic2.0))) |
| 939 | |
| 940 | \f |
| 941 | ;;; Experiment data |
| 942 | |
| 943 | (define-public r-abadata |
| 944 | (package |
| 945 | (name "r-abadata") |
| 946 | (version "1.12.0") |
| 947 | (source (origin |
| 948 | (method url-fetch) |
| 949 | (uri (bioconductor-uri "ABAData" version 'experiment)) |
| 950 | (sha256 |
| 951 | (base32 |
| 952 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) |
| 953 | (properties |
| 954 | `((upstream-name . "ABAData"))) |
| 955 | (build-system r-build-system) |
| 956 | (propagated-inputs |
| 957 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 958 | (home-page "https://www.bioconductor.org/packages/ABAData/") |
| 959 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") |
| 960 | (description |
| 961 | "This package provides the data for the gene expression enrichment |
| 962 | analysis conducted in the package ABAEnrichment. The package includes three |
| 963 | datasets which are derived from the Allen Brain Atlas: |
| 964 | |
| 965 | @enumerate |
| 966 | @item Gene expression data from Human Brain (adults) averaged across donors, |
| 967 | @item Gene expression data from the Developing Human Brain pooled into five |
| 968 | age categories and averaged across donors, and |
| 969 | @item a developmental effect score based on the Developing Human Brain |
| 970 | expression data. |
| 971 | @end enumerate |
| 972 | |
| 973 | All datasets are restricted to protein coding genes.") |
| 974 | (license license:gpl2+))) |
| 975 | |
| 976 | (define-public r-arrmdata |
| 977 | (package |
| 978 | (name "r-arrmdata") |
| 979 | (version "1.18.0") |
| 980 | (source (origin |
| 981 | (method url-fetch) |
| 982 | (uri (bioconductor-uri "ARRmData" version 'experiment)) |
| 983 | (sha256 |
| 984 | (base32 |
| 985 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) |
| 986 | (properties |
| 987 | `((upstream-name . "ARRmData"))) |
| 988 | (build-system r-build-system) |
| 989 | (home-page "https://www.bioconductor.org/packages/ARRmData/") |
| 990 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") |
| 991 | (description |
| 992 | "This package provides raw beta values from 36 samples across 3 groups |
| 993 | from Illumina 450k methylation arrays.") |
| 994 | (license license:artistic2.0))) |
| 995 | |
| 996 | (define-public r-hsmmsinglecell |
| 997 | (package |
| 998 | (name "r-hsmmsinglecell") |
| 999 | (version "1.2.0") |
| 1000 | (source (origin |
| 1001 | (method url-fetch) |
| 1002 | (uri (bioconductor-uri "HSMMSingleCell" version 'experiment)) |
| 1003 | (sha256 |
| 1004 | (base32 |
| 1005 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) |
| 1006 | (properties |
| 1007 | `((upstream-name . "HSMMSingleCell"))) |
| 1008 | (build-system r-build-system) |
| 1009 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") |
| 1010 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") |
| 1011 | (description |
| 1012 | "Skeletal myoblasts undergo a well-characterized sequence of |
| 1013 | morphological and transcriptional changes during differentiation. In this |
| 1014 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded |
| 1015 | under high mitogen conditions (GM) and then differentiated by switching to |
| 1016 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several |
| 1017 | hundred cells taken over a time-course of serum-induced differentiation. |
| 1018 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, |
| 1019 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. |
| 1020 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, |
| 1021 | which were then sequenced to a depth of ~4 million reads per library, |
| 1022 | resulting in a complete gene expression profile for each cell.") |
| 1023 | (license license:artistic2.0))) |
| 1024 | |
| 1025 | (define-public r-all |
| 1026 | (package |
| 1027 | (name "r-all") |
| 1028 | (version "1.26.0") |
| 1029 | (source (origin |
| 1030 | (method url-fetch) |
| 1031 | (uri (bioconductor-uri "ALL" version 'experiment)) |
| 1032 | (sha256 |
| 1033 | (base32 |
| 1034 | "1z7kpjw4ndj6fkxwvhqf3gawhrn26ksrlns7j2c78qzxqmjndik9")))) |
| 1035 | (properties `((upstream-name . "ALL"))) |
| 1036 | (build-system r-build-system) |
| 1037 | (propagated-inputs |
| 1038 | `(("r-biobase" ,r-biobase))) |
| 1039 | (home-page "https://bioconductor.org/packages/ALL") |
| 1040 | (synopsis "Acute Lymphoblastic Leukemia data from the Ritz laboratory") |
| 1041 | (description |
| 1042 | "The data consist of microarrays from 128 different individuals with |
| 1043 | @dfn{acute lymphoblastic leukemia} (ALL). A number of additional covariates |
| 1044 | are available. The data have been normalized (using rma) and it is the |
| 1045 | jointly normalized data that are available here. The data are presented in |
| 1046 | the form of an @code{exprSet} object.") |
| 1047 | (license license:artistic2.0))) |
| 1048 | |
| 1049 | (define-public r-affydata |
| 1050 | (package |
| 1051 | (name "r-affydata") |
| 1052 | (version "1.32.0") |
| 1053 | (source |
| 1054 | (origin |
| 1055 | (method url-fetch) |
| 1056 | (uri (bioconductor-uri "affydata" version 'experiment)) |
| 1057 | (sha256 |
| 1058 | (base32 |
| 1059 | "1l9qhmjqgbrdl9cmd74rlnvmvr6mslbmckb83n0211whp2i0b7h5")))) |
| 1060 | (properties `((upstream-name . "affydata"))) |
| 1061 | (build-system r-build-system) |
| 1062 | (propagated-inputs |
| 1063 | `(("r-affy" ,r-affy))) |
| 1064 | (home-page "https://bioconductor.org/packages/affydata/") |
| 1065 | (synopsis "Affymetrix data for demonstration purposes") |
| 1066 | (description |
| 1067 | "This package provides example datasets that represent 'real world |
| 1068 | examples' of Affymetrix data, unlike the artificial examples included in the |
| 1069 | package @code{affy}.") |
| 1070 | (license license:gpl2+))) |
| 1071 | |
| 1072 | (define-public r-coverageview |
| 1073 | (package |
| 1074 | (name "r-coverageview") |
| 1075 | (version "1.26.0") |
| 1076 | (source (origin |
| 1077 | (method url-fetch) |
| 1078 | (uri (bioconductor-uri "CoverageView" version)) |
| 1079 | (sha256 |
| 1080 | (base32 |
| 1081 | "1fcz7pkffz5l3jdxb9glji2zdmr6nx67h6vfpr2yi8n3slg2hrrj")))) |
| 1082 | (build-system r-build-system) |
| 1083 | (propagated-inputs |
| 1084 | `(("r-s4vectors" ,r-s4vectors) |
| 1085 | ("r-iranges" ,r-iranges) |
| 1086 | ("r-genomicranges" ,r-genomicranges) |
| 1087 | ("r-genomicalignments" ,r-genomicalignments) |
| 1088 | ("r-rtracklayer" ,r-rtracklayer) |
| 1089 | ("r-rsamtools" ,r-rsamtools))) |
| 1090 | (home-page "https://bioconductor.org/packages/CoverageView/") |
| 1091 | (synopsis "Coverage visualization package for R") |
| 1092 | (description "This package provides a framework for the visualization of |
| 1093 | genome coverage profiles. It can be used for ChIP-seq experiments, but it can |
| 1094 | be also used for genome-wide nucleosome positioning experiments or other |
| 1095 | experiment types where it is important to have a framework in order to inspect |
| 1096 | how the coverage distributed across the genome.") |
| 1097 | (license license:artistic2.0))) |
| 1098 | |
| 1099 | (define-public r-cummerbund |
| 1100 | (package |
| 1101 | (name "r-cummerbund") |
| 1102 | (version "2.30.0") |
| 1103 | (source (origin |
| 1104 | (method url-fetch) |
| 1105 | (uri (bioconductor-uri "cummeRbund" version)) |
| 1106 | (sha256 |
| 1107 | (base32 |
| 1108 | "1av7yfxcq1wwbqfqcz7caiz5kf6kg5wq9qcg5v6yccihclzwvxjc")))) |
| 1109 | (build-system r-build-system) |
| 1110 | (propagated-inputs |
| 1111 | `(("r-biobase" ,r-biobase) |
| 1112 | ("r-biocgenerics" ,r-biocgenerics) |
| 1113 | ("r-fastcluster", r-fastcluster) |
| 1114 | ("r-ggplot2" ,r-ggplot2) |
| 1115 | ("r-gviz" ,r-gviz) |
| 1116 | ("r-plyr" ,r-plyr) |
| 1117 | ("r-reshape2" ,r-reshape2) |
| 1118 | ("r-rsqlite" ,r-rsqlite) |
| 1119 | ("r-rtracklayer" ,r-rtracklayer) |
| 1120 | ("r-s4vectors" ,r-s4vectors))) |
| 1121 | (home-page "https://bioconductor.org/packages/cummeRbund/") |
| 1122 | (synopsis "Analyze Cufflinks high-throughput sequencing data") |
| 1123 | (description "This package allows for persistent storage, access, |
| 1124 | exploration, and manipulation of Cufflinks high-throughput sequencing |
| 1125 | data. In addition, provides numerous plotting functions for commonly |
| 1126 | used visualizations.") |
| 1127 | (license license:artistic2.0))) |
| 1128 | |
| 1129 | (define-public r-curatedtcgadata |
| 1130 | (package |
| 1131 | (name "r-curatedtcgadata") |
| 1132 | (version "1.8.0") |
| 1133 | (source |
| 1134 | (origin |
| 1135 | (method url-fetch) |
| 1136 | (uri (bioconductor-uri "curatedTCGAData" version 'experiment)) |
| 1137 | (sha256 |
| 1138 | (base32 |
| 1139 | "02y6cgihmsl9b4a9mmcdjjgjp06lpz04biyvxd3n5lk5gnqd9r3y")))) |
| 1140 | (properties |
| 1141 | `((upstream-name . "curatedTCGAData"))) |
| 1142 | (build-system r-build-system) |
| 1143 | (propagated-inputs |
| 1144 | `(("r-annotationhub" ,r-annotationhub) |
| 1145 | ("r-experimenthub" ,r-experimenthub) |
| 1146 | ("r-hdf5array" ,r-hdf5array) |
| 1147 | ("r-multiassayexperiment" ,r-multiassayexperiment) |
| 1148 | ("r-s4vectors" ,r-s4vectors) |
| 1149 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 1150 | (home-page "https://bioconductor.org/packages/curatedTCGAData/") |
| 1151 | (synopsis "Curated data from The Cancer Genome Atlas") |
| 1152 | (description |
| 1153 | "This package provides publicly available data from The Cancer Genome |
| 1154 | Atlas (TCGA) as @code{MultiAssayExperiment} objects. |
| 1155 | @code{MultiAssayExperiment} integrates multiple assays (e.g., RNA-seq, copy |
| 1156 | number, mutation, microRNA, protein, and others) with clinical / pathological |
| 1157 | data. It also links assay barcodes with patient identifiers, enabling |
| 1158 | harmonized subsetting of rows (features) and columns (patients / samples) |
| 1159 | across the entire multi-'omics experiment.") |
| 1160 | (license license:artistic2.0))) |
| 1161 | |
| 1162 | \f |
| 1163 | ;;; Packages |
| 1164 | |
| 1165 | (define-public r-biocversion |
| 1166 | (package |
| 1167 | (name "r-biocversion") |
| 1168 | (version "3.11.1") |
| 1169 | (source |
| 1170 | (origin |
| 1171 | (method url-fetch) |
| 1172 | (uri (bioconductor-uri "BiocVersion" version)) |
| 1173 | (sha256 |
| 1174 | (base32 |
| 1175 | "1rrzx3dqds0jlj1bmjc744wiamb2hssbh3jfxz1s9jp4cvnwrpmz")))) |
| 1176 | (properties `((upstream-name . "BiocVersion"))) |
| 1177 | (build-system r-build-system) |
| 1178 | (home-page "https://bioconductor.org/packages/BiocVersion/") |
| 1179 | (synopsis "Set the appropriate version of Bioconductor packages") |
| 1180 | (description |
| 1181 | "This package provides repository information for the appropriate version |
| 1182 | of Bioconductor.") |
| 1183 | (license license:artistic2.0))) |
| 1184 | |
| 1185 | (define-public r-biocgenerics |
| 1186 | (package |
| 1187 | (name "r-biocgenerics") |
| 1188 | (version "0.34.0") |
| 1189 | (source (origin |
| 1190 | (method url-fetch) |
| 1191 | (uri (bioconductor-uri "BiocGenerics" version)) |
| 1192 | (sha256 |
| 1193 | (base32 |
| 1194 | "15nvqyh2gx5zkn1krbs5c4rhw5642bijdfsf2rgic70gzr05cksk")))) |
| 1195 | (properties |
| 1196 | `((upstream-name . "BiocGenerics"))) |
| 1197 | (build-system r-build-system) |
| 1198 | (home-page "https://bioconductor.org/packages/BiocGenerics") |
| 1199 | (synopsis "S4 generic functions for Bioconductor") |
| 1200 | (description |
| 1201 | "This package provides S4 generic functions needed by many Bioconductor |
| 1202 | packages.") |
| 1203 | (license license:artistic2.0))) |
| 1204 | |
| 1205 | (define-public r-affycomp |
| 1206 | (package |
| 1207 | (name "r-affycomp") |
| 1208 | (version "1.64.0") |
| 1209 | (source |
| 1210 | (origin |
| 1211 | (method url-fetch) |
| 1212 | (uri (bioconductor-uri "affycomp" version)) |
| 1213 | (sha256 |
| 1214 | (base32 |
| 1215 | "0zg8dshas5b2ny4pnxxxqihnr4l20666ivrgglb939a23mplgps0")))) |
| 1216 | (properties `((upstream-name . "affycomp"))) |
| 1217 | (build-system r-build-system) |
| 1218 | (propagated-inputs `(("r-biobase" ,r-biobase))) |
| 1219 | (home-page "https://bioconductor.org/packages/affycomp/") |
| 1220 | (synopsis "Graphics toolbox for assessment of Affymetrix expression measures") |
| 1221 | (description |
| 1222 | "The package contains functions that can be used to compare expression |
| 1223 | measures for Affymetrix Oligonucleotide Arrays.") |
| 1224 | (license license:gpl2+))) |
| 1225 | |
| 1226 | (define-public r-affycompatible |
| 1227 | (package |
| 1228 | (name "r-affycompatible") |
| 1229 | (version "1.48.0") |
| 1230 | (source |
| 1231 | (origin |
| 1232 | (method url-fetch) |
| 1233 | (uri (bioconductor-uri "AffyCompatible" version)) |
| 1234 | (sha256 |
| 1235 | (base32 |
| 1236 | "0394sr4spafhfypjsafwjr0y0zsgv52ajdcyvsmkdk7375898lqd")))) |
| 1237 | (properties |
| 1238 | `((upstream-name . "AffyCompatible"))) |
| 1239 | (build-system r-build-system) |
| 1240 | (propagated-inputs |
| 1241 | `(("r-biostrings" ,r-biostrings) |
| 1242 | ("r-rcurl" ,r-rcurl) |
| 1243 | ("r-xml" ,r-xml))) |
| 1244 | (home-page "https://bioconductor.org/packages/AffyCompatible/") |
| 1245 | (synopsis "Work with Affymetrix GeneChip files") |
| 1246 | (description |
| 1247 | "This package provides an interface to Affymetrix chip annotation and |
| 1248 | sample attribute files. The package allows an easy way for users to download |
| 1249 | and manage local data bases of Affynmetrix NetAffx annotation files. It also |
| 1250 | provides access to @dfn{GeneChip Operating System} (GCOS) and @dfn{GeneChip |
| 1251 | Command Console} (AGCC)-compatible sample annotation files.") |
| 1252 | (license license:artistic2.0))) |
| 1253 | |
| 1254 | (define-public r-affycontam |
| 1255 | (package |
| 1256 | (name "r-affycontam") |
| 1257 | (version "1.46.0") |
| 1258 | (source |
| 1259 | (origin |
| 1260 | (method url-fetch) |
| 1261 | (uri (bioconductor-uri "affyContam" version)) |
| 1262 | (sha256 |
| 1263 | (base32 |
| 1264 | "1dh5c3blk2dl9kg13y6snplnx61x2f9hvp5lc7jmg25xk916517i")))) |
| 1265 | (properties `((upstream-name . "affyContam"))) |
| 1266 | (build-system r-build-system) |
| 1267 | (propagated-inputs |
| 1268 | `(("r-affy" ,r-affy) |
| 1269 | ("r-affydata" ,r-affydata) |
| 1270 | ("r-biobase" ,r-biobase))) |
| 1271 | (home-page "https://bioconductor.org/packages/affyContam/") |
| 1272 | (synopsis "Structured corruption of Affymetrix CEL file data") |
| 1273 | (description |
| 1274 | "Microarray quality assessment is a major concern of microarray analysts. |
| 1275 | This package provides some simple approaches to in silico creation of quality |
| 1276 | problems in CEL-level data to help evaluate performance of quality metrics.") |
| 1277 | (license license:artistic2.0))) |
| 1278 | |
| 1279 | (define-public r-affycoretools |
| 1280 | (package |
| 1281 | (name "r-affycoretools") |
| 1282 | (version "1.60.1") |
| 1283 | (source |
| 1284 | (origin |
| 1285 | (method url-fetch) |
| 1286 | (uri (bioconductor-uri "affycoretools" version)) |
| 1287 | (sha256 |
| 1288 | (base32 |
| 1289 | "0cnb54b3kmg9rnycvaz949bdali9n98qzrw7gwka6abmg1lv232s")))) |
| 1290 | (properties `((upstream-name . "affycoretools"))) |
| 1291 | (build-system r-build-system) |
| 1292 | (propagated-inputs |
| 1293 | `(("r-affy" ,r-affy) |
| 1294 | ("r-annotationdbi" ,r-annotationdbi) |
| 1295 | ("r-biobase" ,r-biobase) |
| 1296 | ("r-biocgenerics" ,r-biocgenerics) |
| 1297 | ("r-dbi" ,r-dbi) |
| 1298 | ("r-edger" ,r-edger) |
| 1299 | ("r-gcrma" ,r-gcrma) |
| 1300 | ("r-glimma" ,r-glimma) |
| 1301 | ("r-ggplot2" ,r-ggplot2) |
| 1302 | ("r-gostats" ,r-gostats) |
| 1303 | ("r-gplots" ,r-gplots) |
| 1304 | ("r-hwriter" ,r-hwriter) |
| 1305 | ("r-lattice" ,r-lattice) |
| 1306 | ("r-limma" ,r-limma) |
| 1307 | ("r-oligoclasses" ,r-oligoclasses) |
| 1308 | ("r-reportingtools" ,r-reportingtools) |
| 1309 | ("r-rsqlite" ,r-rsqlite) |
| 1310 | ("r-s4vectors" ,r-s4vectors) |
| 1311 | ("r-xtable" ,r-xtable))) |
| 1312 | (native-inputs |
| 1313 | `(("r-knitr" ,r-knitr))) |
| 1314 | (home-page "https://bioconductor.org/packages/affycoretools/") |
| 1315 | (synopsis "Functions for analyses with Affymetrix GeneChips") |
| 1316 | (description |
| 1317 | "This package provides various wrapper functions that have been written |
| 1318 | to streamline the more common analyses that a Biostatistician might see.") |
| 1319 | (license license:artistic2.0))) |
| 1320 | |
| 1321 | (define-public r-affxparser |
| 1322 | (package |
| 1323 | (name "r-affxparser") |
| 1324 | (version "1.60.0") |
| 1325 | (source |
| 1326 | (origin |
| 1327 | (method url-fetch) |
| 1328 | (uri (bioconductor-uri "affxparser" version)) |
| 1329 | (sha256 |
| 1330 | (base32 |
| 1331 | "0d4hq1w0a3dm4bg9qsv7wqrbv2y7b9gllxfmnqs9n2nnwmvgi8yq")))) |
| 1332 | (properties `((upstream-name . "affxparser"))) |
| 1333 | (build-system r-build-system) |
| 1334 | (home-page "https://github.com/HenrikBengtsson/affxparser") |
| 1335 | (synopsis "Affymetrix File Parsing SDK") |
| 1336 | (description |
| 1337 | "This is a package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, |
| 1338 | BAR). It provides methods for fast and memory efficient parsing of Affymetrix |
| 1339 | files using the Affymetrix' Fusion SDK. Both ASCII- and binary-based files |
| 1340 | are supported. Currently, there are methods for reading @dfn{chip definition |
| 1341 | file} (CDF) and a @dfn{cell intensity file} (CEL). These files can be read |
| 1342 | either in full or in part. For example, probe signals from a few probesets |
| 1343 | can be extracted very quickly from a set of CEL files into a convenient list |
| 1344 | structure.") |
| 1345 | ;; The Fusion SDK contains files under GPLv2 and LGPLv2.1. The R code is |
| 1346 | ;; under LGPLv2+. |
| 1347 | (license (list license:lgpl2.0+ license:lgpl2.1 license:gpl2)))) |
| 1348 | |
| 1349 | (define-public r-annotate |
| 1350 | (package |
| 1351 | (name "r-annotate") |
| 1352 | (version "1.66.0") |
| 1353 | (source |
| 1354 | (origin |
| 1355 | (method url-fetch) |
| 1356 | (uri (bioconductor-uri "annotate" version)) |
| 1357 | (sha256 |
| 1358 | (base32 |
| 1359 | "1ivszqknryq6n5a85z8zj12fvgcs6zz3zlza8q08pl6cs4m5rm4w")))) |
| 1360 | (build-system r-build-system) |
| 1361 | (propagated-inputs |
| 1362 | `(("r-annotationdbi" ,r-annotationdbi) |
| 1363 | ("r-biobase" ,r-biobase) |
| 1364 | ("r-biocgenerics" ,r-biocgenerics) |
| 1365 | ("r-dbi" ,r-dbi) |
| 1366 | ("r-rcurl" ,r-rcurl) |
| 1367 | ("r-xml" ,r-xml) |
| 1368 | ("r-xtable" ,r-xtable))) |
| 1369 | (home-page |
| 1370 | "https://bioconductor.org/packages/annotate") |
| 1371 | (synopsis "Annotation for microarrays") |
| 1372 | (description "This package provides R environments for the annotation of |
| 1373 | microarrays.") |
| 1374 | (license license:artistic2.0))) |
| 1375 | |
| 1376 | (define-public r-hpar |
| 1377 | (package |
| 1378 | (name "r-hpar") |
| 1379 | (version "1.30.0") |
| 1380 | (source |
| 1381 | (origin |
| 1382 | (method url-fetch) |
| 1383 | (uri (bioconductor-uri "hpar" version)) |
| 1384 | (sha256 |
| 1385 | (base32 |
| 1386 | "1jq0qw7wq3426cp004divywjm3ryixkykcmwlhrri13agz6rx3r9")))) |
| 1387 | (build-system r-build-system) |
| 1388 | (native-inputs |
| 1389 | `(("r-knitr" ,r-knitr))) |
| 1390 | (home-page "https://bioconductor.org/packages/hpar/") |
| 1391 | (synopsis "Human Protein Atlas in R") |
| 1392 | (description "This package provides a simple interface to and data from |
| 1393 | the Human Protein Atlas project.") |
| 1394 | (license license:artistic2.0))) |
| 1395 | |
| 1396 | (define-public r-regioner |
| 1397 | (package |
| 1398 | (name "r-regioner") |
| 1399 | (version "1.20.0") |
| 1400 | (source |
| 1401 | (origin |
| 1402 | (method url-fetch) |
| 1403 | (uri (bioconductor-uri "regioneR" version)) |
| 1404 | (sha256 |
| 1405 | (base32 |
| 1406 | "10i21gxv0n7lrflhj5ja672xjizy1i4y4iq3pmjgbf0dpy1lxsih")))) |
| 1407 | (properties `((upstream-name . "regioneR"))) |
| 1408 | (build-system r-build-system) |
| 1409 | (propagated-inputs |
| 1410 | `(("r-biostrings" ,r-biostrings) |
| 1411 | ("r-bsgenome" ,r-bsgenome) |
| 1412 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1413 | ("r-genomicranges" ,r-genomicranges) |
| 1414 | ("r-iranges" ,r-iranges) |
| 1415 | ("r-memoise" ,r-memoise) |
| 1416 | ("r-rtracklayer" ,r-rtracklayer) |
| 1417 | ("r-s4vectors" ,r-s4vectors))) |
| 1418 | (native-inputs |
| 1419 | `(("r-knitr" ,r-knitr))) |
| 1420 | (home-page "https://bioconductor.org/packages/regioneR/") |
| 1421 | (synopsis "Association analysis of genomic regions") |
| 1422 | (description "This package offers a statistical framework based on |
| 1423 | customizable permutation tests to assess the association between genomic |
| 1424 | region sets and other genomic features.") |
| 1425 | (license license:artistic2.0))) |
| 1426 | |
| 1427 | (define-public r-reportingtools |
| 1428 | (package |
| 1429 | (name "r-reportingtools") |
| 1430 | (version "2.28.0") |
| 1431 | (source |
| 1432 | (origin |
| 1433 | (method url-fetch) |
| 1434 | (uri (bioconductor-uri "ReportingTools" version)) |
| 1435 | (sha256 |
| 1436 | (base32 |
| 1437 | "1ig1h224silbdbdr0j9j9sysp9l9dzpcsjzn8jp57h3gh4pdqbfx")))) |
| 1438 | (properties |
| 1439 | `((upstream-name . "ReportingTools"))) |
| 1440 | (build-system r-build-system) |
| 1441 | (propagated-inputs |
| 1442 | `(("r-annotate" ,r-annotate) |
| 1443 | ("r-annotationdbi" ,r-annotationdbi) |
| 1444 | ("r-biobase" ,r-biobase) |
| 1445 | ("r-biocgenerics" ,r-biocgenerics) |
| 1446 | ("r-category" ,r-category) |
| 1447 | ("r-deseq2" ,r-deseq2) |
| 1448 | ("r-edger" ,r-edger) |
| 1449 | ("r-ggbio" ,r-ggbio) |
| 1450 | ("r-ggplot2" ,r-ggplot2) |
| 1451 | ("r-gostats" ,r-gostats) |
| 1452 | ("r-gseabase" ,r-gseabase) |
| 1453 | ("r-hwriter" ,r-hwriter) |
| 1454 | ("r-iranges" ,r-iranges) |
| 1455 | ("r-knitr" ,r-knitr) |
| 1456 | ("r-lattice" ,r-lattice) |
| 1457 | ("r-limma" ,r-limma) |
| 1458 | ("r-pfam-db" ,r-pfam-db) |
| 1459 | ("r-r-utils" ,r-r-utils) |
| 1460 | ("r-xml" ,r-xml))) |
| 1461 | (native-inputs |
| 1462 | `(("r-knitr" ,r-knitr))) |
| 1463 | (home-page "https://bioconductor.org/packages/ReportingTools/") |
| 1464 | (synopsis "Tools for making reports in various formats") |
| 1465 | (description |
| 1466 | "The ReportingTools package enables users to easily display reports of |
| 1467 | analysis results generated from sources such as microarray and sequencing |
| 1468 | data. The package allows users to create HTML pages that may be viewed on a |
| 1469 | web browser, or in other formats. Users can generate tables with sortable and |
| 1470 | filterable columns, make and display plots, and link table entries to other |
| 1471 | data sources such as NCBI or larger plots within the HTML page. Using the |
| 1472 | package, users can also produce a table of contents page to link various |
| 1473 | reports together for a particular project that can be viewed in a web |
| 1474 | browser.") |
| 1475 | (license license:artistic2.0))) |
| 1476 | |
| 1477 | (define-public r-geneplotter |
| 1478 | (package |
| 1479 | (name "r-geneplotter") |
| 1480 | (version "1.66.0") |
| 1481 | (source |
| 1482 | (origin |
| 1483 | (method url-fetch) |
| 1484 | (uri (bioconductor-uri "geneplotter" version)) |
| 1485 | (sha256 |
| 1486 | (base32 |
| 1487 | "1y494da1llmrvn3qm7akwgwjazvpffabi8llw3fbday14cay1br5")))) |
| 1488 | (build-system r-build-system) |
| 1489 | (propagated-inputs |
| 1490 | `(("r-annotate" ,r-annotate) |
| 1491 | ("r-annotationdbi" ,r-annotationdbi) |
| 1492 | ("r-biobase" ,r-biobase) |
| 1493 | ("r-biocgenerics" ,r-biocgenerics) |
| 1494 | ("r-lattice" ,r-lattice) |
| 1495 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 1496 | (home-page "https://bioconductor.org/packages/geneplotter") |
| 1497 | (synopsis "Graphics functions for genomic data") |
| 1498 | (description |
| 1499 | "This package provides functions for plotting genomic data.") |
| 1500 | (license license:artistic2.0))) |
| 1501 | |
| 1502 | (define-public r-oligoclasses |
| 1503 | (package |
| 1504 | (name "r-oligoclasses") |
| 1505 | (version "1.50.0") |
| 1506 | (source |
| 1507 | (origin |
| 1508 | (method url-fetch) |
| 1509 | (uri (bioconductor-uri "oligoClasses" version)) |
| 1510 | (sha256 |
| 1511 | (base32 |
| 1512 | "05jy9qz3ir4maxackr1xqlfi1czhy1qd22wwibjdhfh5dp534cpn")))) |
| 1513 | (properties `((upstream-name . "oligoClasses"))) |
| 1514 | (build-system r-build-system) |
| 1515 | (propagated-inputs |
| 1516 | `(("r-affyio" ,r-affyio) |
| 1517 | ("r-biobase" ,r-biobase) |
| 1518 | ("r-biocgenerics" ,r-biocgenerics) |
| 1519 | ("r-biocmanager" ,r-biocmanager) |
| 1520 | ("r-biostrings" ,r-biostrings) |
| 1521 | ("r-dbi" ,r-dbi) |
| 1522 | ("r-ff" ,r-ff) |
| 1523 | ("r-foreach" ,r-foreach) |
| 1524 | ("r-genomicranges" ,r-genomicranges) |
| 1525 | ("r-iranges" ,r-iranges) |
| 1526 | ("r-rsqlite" ,r-rsqlite) |
| 1527 | ("r-s4vectors" ,r-s4vectors) |
| 1528 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 1529 | (home-page "https://bioconductor.org/packages/oligoClasses/") |
| 1530 | (synopsis "Classes for high-throughput arrays") |
| 1531 | (description |
| 1532 | "This package contains class definitions, validity checks, and |
| 1533 | initialization methods for classes used by the @code{oligo} and @code{crlmm} |
| 1534 | packages.") |
| 1535 | (license license:gpl2+))) |
| 1536 | |
| 1537 | (define-public r-oligo |
| 1538 | (package |
| 1539 | (name "r-oligo") |
| 1540 | (version "1.52.0") |
| 1541 | (source |
| 1542 | (origin |
| 1543 | (method url-fetch) |
| 1544 | (uri (bioconductor-uri "oligo" version)) |
| 1545 | (sha256 |
| 1546 | (base32 |
| 1547 | "102szyiicws4c6l3k282236ml1m1vl9zmars4q1kdjfnvsyclfc4")))) |
| 1548 | (properties `((upstream-name . "oligo"))) |
| 1549 | (build-system r-build-system) |
| 1550 | (inputs `(("zlib" ,zlib))) |
| 1551 | (propagated-inputs |
| 1552 | `(("r-affxparser" ,r-affxparser) |
| 1553 | ("r-affyio" ,r-affyio) |
| 1554 | ("r-biobase" ,r-biobase) |
| 1555 | ("r-biocgenerics" ,r-biocgenerics) |
| 1556 | ("r-biostrings" ,r-biostrings) |
| 1557 | ("r-dbi" ,r-dbi) |
| 1558 | ("r-ff" ,r-ff) |
| 1559 | ("r-oligoclasses" ,r-oligoclasses) |
| 1560 | ("r-preprocesscore" ,r-preprocesscore) |
| 1561 | ("r-rsqlite" ,r-rsqlite) |
| 1562 | ("r-zlibbioc" ,r-zlibbioc))) |
| 1563 | (native-inputs |
| 1564 | `(("r-knitr" ,r-knitr))) |
| 1565 | (home-page "https://bioconductor.org/packages/oligo/") |
| 1566 | (synopsis "Preprocessing tools for oligonucleotide arrays") |
| 1567 | (description |
| 1568 | "This package provides a package to analyze oligonucleotide |
| 1569 | arrays (expression/SNP/tiling/exon) at probe-level. It currently supports |
| 1570 | Affymetrix (CEL files) and NimbleGen arrays (XYS files).") |
| 1571 | (license license:lgpl2.0+))) |
| 1572 | |
| 1573 | (define-public r-qvalue |
| 1574 | (package |
| 1575 | (name "r-qvalue") |
| 1576 | (version "2.20.0") |
| 1577 | (source |
| 1578 | (origin |
| 1579 | (method url-fetch) |
| 1580 | (uri (bioconductor-uri "qvalue" version)) |
| 1581 | (sha256 |
| 1582 | (base32 |
| 1583 | "1hndmdr9niagbr4ry0vbhffvjzjg9im27kdbn0sa774k6r5b4z3f")))) |
| 1584 | (build-system r-build-system) |
| 1585 | (propagated-inputs |
| 1586 | `(("r-ggplot2" ,r-ggplot2) |
| 1587 | ("r-reshape2" ,r-reshape2))) |
| 1588 | (native-inputs |
| 1589 | `(("r-knitr" ,r-knitr))) |
| 1590 | (home-page "http://github.com/jdstorey/qvalue") |
| 1591 | (synopsis "Q-value estimation for false discovery rate control") |
| 1592 | (description |
| 1593 | "This package takes a list of p-values resulting from the simultaneous |
| 1594 | testing of many hypotheses and estimates their q-values and local @dfn{false |
| 1595 | discovery rate} (FDR) values. The q-value of a test measures the proportion |
| 1596 | of false positives incurred when that particular test is called significant. |
| 1597 | The local FDR measures the posterior probability the null hypothesis is true |
| 1598 | given the test's p-value. Various plots are automatically generated, allowing |
| 1599 | one to make sensible significance cut-offs. The software can be applied to |
| 1600 | problems in genomics, brain imaging, astrophysics, and data mining.") |
| 1601 | ;; Any version of the LGPL. |
| 1602 | (license license:lgpl3+))) |
| 1603 | |
| 1604 | (define-public r-diffbind |
| 1605 | (package |
| 1606 | (name "r-diffbind") |
| 1607 | (version "2.16.0") |
| 1608 | (source |
| 1609 | (origin |
| 1610 | (method url-fetch) |
| 1611 | (uri (bioconductor-uri "DiffBind" version)) |
| 1612 | (sha256 |
| 1613 | (base32 |
| 1614 | "1mwqgljya1c7r2dfrdds3nswn9bn1l3ak1wavbpv4lbv3nkmykn5")))) |
| 1615 | (properties `((upstream-name . "DiffBind"))) |
| 1616 | (build-system r-build-system) |
| 1617 | (inputs |
| 1618 | `(("zlib" ,zlib))) |
| 1619 | (propagated-inputs |
| 1620 | `(("r-amap" ,r-amap) |
| 1621 | ("r-biocparallel" ,r-biocparallel) |
| 1622 | ("r-deseq2" ,r-deseq2) |
| 1623 | ("r-dplyr" ,r-dplyr) |
| 1624 | ("r-edger" ,r-edger) |
| 1625 | ("r-genomicalignments" ,r-genomicalignments) |
| 1626 | ("r-genomicranges" ,r-genomicranges) |
| 1627 | ("r-ggplot2" ,r-ggplot2) |
| 1628 | ("r-ggrepel" ,r-ggrepel) |
| 1629 | ("r-gplots" ,r-gplots) |
| 1630 | ("r-iranges" ,r-iranges) |
| 1631 | ("r-lattice" ,r-lattice) |
| 1632 | ("r-limma" ,r-limma) |
| 1633 | ("r-locfit" ,r-locfit) |
| 1634 | ("r-rcolorbrewer" , r-rcolorbrewer) |
| 1635 | ("r-rcpp" ,r-rcpp) |
| 1636 | ("r-rhtslib" ,r-rhtslib) |
| 1637 | ("r-rsamtools" ,r-rsamtools) |
| 1638 | ("r-s4vectors" ,r-s4vectors) |
| 1639 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 1640 | ("r-systempiper" ,r-systempiper))) |
| 1641 | (home-page "https://bioconductor.org/packages/DiffBind") |
| 1642 | (synopsis "Differential binding analysis of ChIP-Seq peak data") |
| 1643 | (description |
| 1644 | "This package computes differentially bound sites from multiple |
| 1645 | ChIP-seq experiments using affinity (quantitative) data. Also enables |
| 1646 | occupancy (overlap) analysis and plotting functions.") |
| 1647 | (license license:artistic2.0))) |
| 1648 | |
| 1649 | (define-public r-ripseeker |
| 1650 | (package |
| 1651 | (name "r-ripseeker") |
| 1652 | (version "1.26.0") |
| 1653 | (source |
| 1654 | (origin |
| 1655 | (method url-fetch) |
| 1656 | (uri (bioconductor-uri "RIPSeeker" version)) |
| 1657 | (sha256 |
| 1658 | (base32 |
| 1659 | "1wyv9mfrbxzklysfjcnwb8yils71janyyxa982jn0zxx4p9cl3vs")))) |
| 1660 | (properties `((upstream-name . "RIPSeeker"))) |
| 1661 | (build-system r-build-system) |
| 1662 | (propagated-inputs |
| 1663 | `(("r-s4vectors" ,r-s4vectors) |
| 1664 | ("r-iranges" ,r-iranges) |
| 1665 | ("r-genomicranges" ,r-genomicranges) |
| 1666 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 1667 | ("r-rsamtools" ,r-rsamtools) |
| 1668 | ("r-genomicalignments" ,r-genomicalignments) |
| 1669 | ("r-rtracklayer" ,r-rtracklayer))) |
| 1670 | (home-page "https://bioconductor.org/packages/RIPSeeker") |
| 1671 | (synopsis |
| 1672 | "Identifying protein-associated transcripts from RIP-seq experiments") |
| 1673 | (description |
| 1674 | "This package infers and discriminates RIP peaks from RIP-seq alignments |
| 1675 | using two-state HMM with negative binomial emission probability. While |
| 1676 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides |
| 1677 | a suite of bioinformatics tools integrated within this self-contained software |
| 1678 | package comprehensively addressing issues ranging from post-alignments |
| 1679 | processing to visualization and annotation.") |
| 1680 | (license license:gpl2))) |
| 1681 | |
| 1682 | (define-public r-multtest |
| 1683 | (package |
| 1684 | (name "r-multtest") |
| 1685 | (version "2.44.0") |
| 1686 | (source |
| 1687 | (origin |
| 1688 | (method url-fetch) |
| 1689 | (uri (bioconductor-uri "multtest" version)) |
| 1690 | (sha256 |
| 1691 | (base32 |
| 1692 | "12li7nzzygm3sjfx472095irqpawixk48d0k591wlnrms6sxchx2")))) |
| 1693 | (build-system r-build-system) |
| 1694 | (propagated-inputs |
| 1695 | `(("r-survival" ,r-survival) |
| 1696 | ("r-biocgenerics" ,r-biocgenerics) |
| 1697 | ("r-biobase" ,r-biobase) |
| 1698 | ("r-mass" ,r-mass))) |
| 1699 | (home-page "https://bioconductor.org/packages/multtest") |
| 1700 | (synopsis "Resampling-based multiple hypothesis testing") |
| 1701 | (description |
| 1702 | "This package can do non-parametric bootstrap and permutation |
| 1703 | resampling-based multiple testing procedures (including empirical Bayes |
| 1704 | methods) for controlling the family-wise error rate (FWER), generalized |
| 1705 | family-wise error rate (gFWER), tail probability of the proportion of |
| 1706 | false positives (TPPFP), and false discovery rate (FDR). Several choices |
| 1707 | of bootstrap-based null distribution are implemented (centered, centered |
| 1708 | and scaled, quantile-transformed). Single-step and step-wise methods are |
| 1709 | available. Tests based on a variety of T- and F-statistics (including |
| 1710 | T-statistics based on regression parameters from linear and survival models |
| 1711 | as well as those based on correlation parameters) are included. When probing |
| 1712 | hypotheses with T-statistics, users may also select a potentially faster null |
| 1713 | distribution which is multivariate normal with mean zero and variance |
| 1714 | covariance matrix derived from the vector influence function. Results are |
| 1715 | reported in terms of adjusted P-values, confidence regions and test statistic |
| 1716 | cutoffs. The procedures are directly applicable to identifying differentially |
| 1717 | expressed genes in DNA microarray experiments.") |
| 1718 | (license license:lgpl3))) |
| 1719 | |
| 1720 | (define-public r-graph |
| 1721 | (package |
| 1722 | (name "r-graph") |
| 1723 | (version "1.66.0") |
| 1724 | (source (origin |
| 1725 | (method url-fetch) |
| 1726 | (uri (bioconductor-uri "graph" version)) |
| 1727 | (sha256 |
| 1728 | (base32 |
| 1729 | "15v0nx9gzpszmdn5lil1s1y8qfmsirlznh56wcyqq4sxwjbyjn9g")))) |
| 1730 | (build-system r-build-system) |
| 1731 | (propagated-inputs |
| 1732 | `(("r-biocgenerics" ,r-biocgenerics))) |
| 1733 | (home-page "https://bioconductor.org/packages/graph") |
| 1734 | (synopsis "Handle graph data structures in R") |
| 1735 | (description |
| 1736 | "This package implements some simple graph handling capabilities for R.") |
| 1737 | (license license:artistic2.0))) |
| 1738 | |
| 1739 | ;; This is a CRAN package, but it depends on a Bioconductor package. |
| 1740 | (define-public r-ggm |
| 1741 | (package |
| 1742 | (name "r-ggm") |
| 1743 | (version "2.5") |
| 1744 | (source |
| 1745 | (origin |
| 1746 | (method url-fetch) |
| 1747 | (uri (cran-uri "ggm" version)) |
| 1748 | (sha256 |
| 1749 | (base32 |
| 1750 | "11wc6k2kj2ydy0dyks5mbvbhxm1r43id87anl1jg6dn0yv4m78di")))) |
| 1751 | (properties `((upstream-name . "ggm"))) |
| 1752 | (build-system r-build-system) |
| 1753 | (propagated-inputs |
| 1754 | `(("r-graph" ,r-graph) |
| 1755 | ("r-igraph" ,r-igraph))) |
| 1756 | (home-page "https://cran.r-project.org/package=ggm") |
| 1757 | (synopsis "Functions for graphical Markov models") |
| 1758 | (description |
| 1759 | "This package provides functions and datasets for maximum likelihood |
| 1760 | fitting of some classes of graphical Markov models.") |
| 1761 | (license license:gpl2+))) |
| 1762 | |
| 1763 | (define-public r-codedepends |
| 1764 | (package |
| 1765 | (name "r-codedepends") |
| 1766 | (version "0.6.5") |
| 1767 | (source |
| 1768 | (origin |
| 1769 | (method url-fetch) |
| 1770 | (uri (cran-uri "CodeDepends" version)) |
| 1771 | (sha256 |
| 1772 | (base32 |
| 1773 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) |
| 1774 | (properties `((upstream-name . "CodeDepends"))) |
| 1775 | (build-system r-build-system) |
| 1776 | (propagated-inputs |
| 1777 | `(("r-codetools" ,r-codetools) |
| 1778 | ("r-graph" ,r-graph) |
| 1779 | ("r-xml" ,r-xml))) |
| 1780 | (home-page "https://cran.r-project.org/web/packages/CodeDepends") |
| 1781 | (synopsis "Analysis of R code for reproducible research and code comprehension") |
| 1782 | (description |
| 1783 | "This package provides tools for analyzing R expressions or blocks of |
| 1784 | code and determining the dependencies between them. It focuses on R scripts, |
| 1785 | but can be used on the bodies of functions. There are many facilities |
| 1786 | including the ability to summarize or get a high-level view of code, |
| 1787 | determining dependencies between variables, code improvement suggestions.") |
| 1788 | ;; Any version of the GPL |
| 1789 | (license (list license:gpl2+ license:gpl3+)))) |
| 1790 | |
| 1791 | (define-public r-chippeakanno |
| 1792 | (package |
| 1793 | (name "r-chippeakanno") |
| 1794 | (version "3.22.2") |
| 1795 | (source |
| 1796 | (origin |
| 1797 | (method url-fetch) |
| 1798 | (uri (bioconductor-uri "ChIPpeakAnno" version)) |
| 1799 | (sha256 |
| 1800 | (base32 |
| 1801 | "199mlg0gwjy39afyk0ah6lzcm759bzxla4hgcajj0ay9jiibjqpa")))) |
| 1802 | (properties `((upstream-name . "ChIPpeakAnno"))) |
| 1803 | (build-system r-build-system) |
| 1804 | (propagated-inputs |
| 1805 | `(("r-annotationdbi" ,r-annotationdbi) |
| 1806 | ("r-biobase" ,r-biobase) |
| 1807 | ("r-biocgenerics" ,r-biocgenerics) |
| 1808 | ("r-biocmanager" ,r-biocmanager) |
| 1809 | ("r-biomart" ,r-biomart) |
| 1810 | ("r-biostrings" ,r-biostrings) |
| 1811 | ("r-bsgenome" ,r-bsgenome) |
| 1812 | ("r-dbi" ,r-dbi) |
| 1813 | ("r-delayedarray" ,r-delayedarray) |
| 1814 | ("r-ensembldb" ,r-ensembldb) |
| 1815 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1816 | ("r-genomicalignments" ,r-genomicalignments) |
| 1817 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 1818 | ("r-genomicranges" ,r-genomicranges) |
| 1819 | ("r-go-db" ,r-go-db) |
| 1820 | ("r-graph" ,r-graph) |
| 1821 | ("r-idr" ,r-idr) |
| 1822 | ("r-iranges" ,r-iranges) |
| 1823 | ("r-limma" ,r-limma) |
| 1824 | ("r-matrixstats" ,r-matrixstats) |
| 1825 | ("r-multtest" ,r-multtest) |
| 1826 | ("r-rbgl" ,r-rbgl) |
| 1827 | ("r-regioner" ,r-regioner) |
| 1828 | ("r-rsamtools" ,r-rsamtools) |
| 1829 | ("r-rtracklayer" ,r-rtracklayer) |
| 1830 | ("r-s4vectors" ,r-s4vectors) |
| 1831 | ("r-seqinr" ,r-seqinr) |
| 1832 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 1833 | ("r-venndiagram" ,r-venndiagram))) |
| 1834 | (native-inputs |
| 1835 | `(("r-knitr" ,r-knitr))) |
| 1836 | (home-page "https://bioconductor.org/packages/ChIPpeakAnno") |
| 1837 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") |
| 1838 | (description |
| 1839 | "The package includes functions to retrieve the sequences around the peak, |
| 1840 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or |
| 1841 | custom features such as most conserved elements and other transcription factor |
| 1842 | binding sites supplied by users. Starting 2.0.5, new functions have been added |
| 1843 | for finding the peaks with bi-directional promoters with summary statistics |
| 1844 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks |
| 1845 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or |
| 1846 | enrichedGO (addGeneIDs).") |
| 1847 | (license license:gpl2+))) |
| 1848 | |
| 1849 | (define-public r-marray |
| 1850 | (package |
| 1851 | (name "r-marray") |
| 1852 | (version "1.66.0") |
| 1853 | (source (origin |
| 1854 | (method url-fetch) |
| 1855 | (uri (bioconductor-uri "marray" version)) |
| 1856 | (sha256 |
| 1857 | (base32 "1sym3nis5qzg05b2in83xr019mvz8czy8qvispc0hzsq42yng6kd")))) |
| 1858 | (build-system r-build-system) |
| 1859 | (propagated-inputs |
| 1860 | `(("r-limma" ,r-limma))) |
| 1861 | (home-page "https://bioconductor.org/packages/marray") |
| 1862 | (synopsis "Exploratory analysis for two-color spotted microarray data") |
| 1863 | (description "This package contains class definitions for two-color spotted |
| 1864 | microarray data. It also includes functions for data input, diagnostic plots, |
| 1865 | normalization and quality checking.") |
| 1866 | (license license:lgpl2.0+))) |
| 1867 | |
| 1868 | (define-public r-cghbase |
| 1869 | (package |
| 1870 | (name "r-cghbase") |
| 1871 | (version "1.48.0") |
| 1872 | (source (origin |
| 1873 | (method url-fetch) |
| 1874 | (uri (bioconductor-uri "CGHbase" version)) |
| 1875 | (sha256 |
| 1876 | (base32 "0gfqqa9rs5hid53ihlky88qndgrwxxz0s6j7s505f660dd5nzlkf")))) |
| 1877 | (properties `((upstream-name . "CGHbase"))) |
| 1878 | (build-system r-build-system) |
| 1879 | (propagated-inputs |
| 1880 | `(("r-biobase" ,r-biobase) |
| 1881 | ("r-marray" ,r-marray))) |
| 1882 | (home-page "https://bioconductor.org/packages/CGHbase") |
| 1883 | (synopsis "Base functions and classes for arrayCGH data analysis") |
| 1884 | (description "This package contains functions and classes that are needed by |
| 1885 | the @code{arrayCGH} packages.") |
| 1886 | (license license:gpl2+))) |
| 1887 | |
| 1888 | (define-public r-cghcall |
| 1889 | (package |
| 1890 | (name "r-cghcall") |
| 1891 | (version "2.50.0") |
| 1892 | (source (origin |
| 1893 | (method url-fetch) |
| 1894 | (uri (bioconductor-uri "CGHcall" version)) |
| 1895 | (sha256 |
| 1896 | (base32 "1dz6sag8khl18vkb97b5w6fk6k9s7s9xxnc467dd3bmhmajlmrrg")))) |
| 1897 | (properties `((upstream-name . "CGHcall"))) |
| 1898 | (build-system r-build-system) |
| 1899 | (propagated-inputs |
| 1900 | `(("r-biobase" ,r-biobase) |
| 1901 | ("r-cghbase" ,r-cghbase) |
| 1902 | ("r-impute" ,r-impute) |
| 1903 | ("r-dnacopy" ,r-dnacopy) |
| 1904 | ("r-snowfall" ,r-snowfall))) |
| 1905 | (home-page "https://bioconductor.org/packages/CGHcall") |
| 1906 | (synopsis "Base functions and classes for arrayCGH data analysis") |
| 1907 | (description "This package contains functions and classes that are needed by |
| 1908 | @code{arrayCGH} packages.") |
| 1909 | (license license:gpl2+))) |
| 1910 | |
| 1911 | (define-public r-qdnaseq |
| 1912 | (package |
| 1913 | (name "r-qdnaseq") |
| 1914 | (version "1.24.0") |
| 1915 | (source (origin |
| 1916 | (method url-fetch) |
| 1917 | (uri (bioconductor-uri "QDNAseq" version)) |
| 1918 | (sha256 |
| 1919 | (base32 "1ji9pl2r1idyj3qzggj7qd2kqx31i6b3igwk2hqjb8qzkyb37p86")))) |
| 1920 | (properties `((upstream-name . "QDNAseq"))) |
| 1921 | (build-system r-build-system) |
| 1922 | (propagated-inputs |
| 1923 | `(("r-biobase" ,r-biobase) |
| 1924 | ("r-cghbase" ,r-cghbase) |
| 1925 | ("r-cghcall" ,r-cghcall) |
| 1926 | ("r-dnacopy" ,r-dnacopy) |
| 1927 | ("r-future" ,r-future) |
| 1928 | ("r-future-apply" ,r-future-apply) |
| 1929 | ("r-genomicranges" ,r-genomicranges) |
| 1930 | ("r-iranges" ,r-iranges) |
| 1931 | ("r-matrixstats" ,r-matrixstats) |
| 1932 | ("r-r-utils" ,r-r-utils) |
| 1933 | ("r-rsamtools" ,r-rsamtools))) |
| 1934 | (home-page "https://bioconductor.org/packages/QDNAseq") |
| 1935 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") |
| 1936 | (description "The genome is divided into non-overlapping fixed-sized bins, |
| 1937 | number of sequence reads in each counted, adjusted with a simultaneous |
| 1938 | two-dimensional loess correction for sequence mappability and GC content, and |
| 1939 | filtered to remove spurious regions in the genome. Downstream steps of |
| 1940 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, |
| 1941 | respectively.") |
| 1942 | (license license:gpl2+))) |
| 1943 | |
| 1944 | (define-public r-bayseq |
| 1945 | (package |
| 1946 | (name "r-bayseq") |
| 1947 | (version "2.22.0") |
| 1948 | (source |
| 1949 | (origin |
| 1950 | (method url-fetch) |
| 1951 | (uri (bioconductor-uri "baySeq" version)) |
| 1952 | (sha256 |
| 1953 | (base32 |
| 1954 | "1x0d34pqv9s15nmmxsfbw0ycxbf5348mi30ahycarjkjsyzycymj")))) |
| 1955 | (properties `((upstream-name . "baySeq"))) |
| 1956 | (build-system r-build-system) |
| 1957 | (propagated-inputs |
| 1958 | `(("r-abind" ,r-abind) |
| 1959 | ("r-edger" ,r-edger) |
| 1960 | ("r-genomicranges" ,r-genomicranges))) |
| 1961 | (home-page "https://bioconductor.org/packages/baySeq/") |
| 1962 | (synopsis "Bayesian analysis of differential expression patterns in count data") |
| 1963 | (description |
| 1964 | "This package identifies differential expression in high-throughput count |
| 1965 | data, such as that derived from next-generation sequencing machines, |
| 1966 | calculating estimated posterior likelihoods of differential expression (or |
| 1967 | more complex hypotheses) via empirical Bayesian methods.") |
| 1968 | (license license:gpl3))) |
| 1969 | |
| 1970 | (define-public r-chipcomp |
| 1971 | (package |
| 1972 | (name "r-chipcomp") |
| 1973 | (version "1.18.0") |
| 1974 | (source |
| 1975 | (origin |
| 1976 | (method url-fetch) |
| 1977 | (uri (bioconductor-uri "ChIPComp" version)) |
| 1978 | (sha256 |
| 1979 | (base32 |
| 1980 | "0780kj9vbzdhf2jkfb1my8m58pcdwk6jqw6zfng82g46jias98cp")))) |
| 1981 | (properties `((upstream-name . "ChIPComp"))) |
| 1982 | (build-system r-build-system) |
| 1983 | (propagated-inputs |
| 1984 | `(("r-biocgenerics" ,r-biocgenerics) |
| 1985 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 1986 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) |
| 1987 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1988 | ("r-genomicranges" ,r-genomicranges) |
| 1989 | ("r-iranges" ,r-iranges) |
| 1990 | ("r-limma" ,r-limma) |
| 1991 | ("r-rsamtools" ,r-rsamtools) |
| 1992 | ("r-rtracklayer" ,r-rtracklayer) |
| 1993 | ("r-s4vectors" ,r-s4vectors))) |
| 1994 | (home-page "https://bioconductor.org/packages/ChIPComp") |
| 1995 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") |
| 1996 | (description |
| 1997 | "ChIPComp implements a statistical method for quantitative comparison of |
| 1998 | multiple ChIP-seq datasets. It detects differentially bound sharp binding |
| 1999 | sites across multiple conditions considering matching control in ChIP-seq |
| 2000 | datasets.") |
| 2001 | ;; Any version of the GPL. |
| 2002 | (license license:gpl3+))) |
| 2003 | |
| 2004 | (define-public r-riboprofiling |
| 2005 | (package |
| 2006 | (name "r-riboprofiling") |
| 2007 | (version "1.18.0") |
| 2008 | (source |
| 2009 | (origin |
| 2010 | (method url-fetch) |
| 2011 | (uri (bioconductor-uri "RiboProfiling" version)) |
| 2012 | (sha256 |
| 2013 | (base32 |
| 2014 | "0s30m96dbbrzbywz3wai5ar0nsshb16lq101nyl20w1bk7sk2bha")))) |
| 2015 | (properties `((upstream-name . "RiboProfiling"))) |
| 2016 | (build-system r-build-system) |
| 2017 | (propagated-inputs |
| 2018 | `(("r-biocgenerics" ,r-biocgenerics) |
| 2019 | ("r-biostrings" ,r-biostrings) |
| 2020 | ("r-data-table" ,r-data-table) |
| 2021 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2022 | ("r-genomicalignments" ,r-genomicalignments) |
| 2023 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 2024 | ("r-genomicranges" ,r-genomicranges) |
| 2025 | ("r-ggbio" ,r-ggbio) |
| 2026 | ("r-ggplot2" ,r-ggplot2) |
| 2027 | ("r-iranges" ,r-iranges) |
| 2028 | ("r-plyr" ,r-plyr) |
| 2029 | ("r-reshape2" ,r-reshape2) |
| 2030 | ("r-rsamtools" ,r-rsamtools) |
| 2031 | ("r-rtracklayer" ,r-rtracklayer) |
| 2032 | ("r-s4vectors" ,r-s4vectors) |
| 2033 | ("r-sqldf" ,r-sqldf))) |
| 2034 | (native-inputs |
| 2035 | `(("r-knitr" ,r-knitr))) |
| 2036 | (home-page "https://bioconductor.org/packages/RiboProfiling/") |
| 2037 | (synopsis "Ribosome profiling data analysis") |
| 2038 | (description "Starting with a BAM file, this package provides the |
| 2039 | necessary functions for quality assessment, read start position recalibration, |
| 2040 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting |
| 2041 | of count data: pairs, log fold-change, codon frequency and coverage |
| 2042 | assessment, principal component analysis on codon coverage.") |
| 2043 | (license license:gpl3))) |
| 2044 | |
| 2045 | (define-public r-riboseqr |
| 2046 | (package |
| 2047 | (name "r-riboseqr") |
| 2048 | (version "1.22.0") |
| 2049 | (source |
| 2050 | (origin |
| 2051 | (method url-fetch) |
| 2052 | (uri (bioconductor-uri "riboSeqR" version)) |
| 2053 | (sha256 |
| 2054 | (base32 |
| 2055 | "04a4dkmacd6xy55m84amxa0fspbc4kgg9r9k7bc3wrxswk77ccxk")))) |
| 2056 | (properties `((upstream-name . "riboSeqR"))) |
| 2057 | (build-system r-build-system) |
| 2058 | (propagated-inputs |
| 2059 | `(("r-abind" ,r-abind) |
| 2060 | ("r-bayseq" ,r-bayseq) |
| 2061 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2062 | ("r-genomicranges" ,r-genomicranges) |
| 2063 | ("r-iranges" ,r-iranges) |
| 2064 | ("r-rsamtools" ,r-rsamtools) |
| 2065 | ("r-seqlogo" ,r-seqlogo))) |
| 2066 | (home-page "https://bioconductor.org/packages/riboSeqR/") |
| 2067 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") |
| 2068 | (description |
| 2069 | "This package provides plotting functions, frameshift detection and |
| 2070 | parsing of genetic sequencing data from ribosome profiling experiments.") |
| 2071 | (license license:gpl3))) |
| 2072 | |
| 2073 | (define-public r-interactionset |
| 2074 | (package |
| 2075 | (name "r-interactionset") |
| 2076 | (version "1.16.0") |
| 2077 | (source |
| 2078 | (origin |
| 2079 | (method url-fetch) |
| 2080 | (uri (bioconductor-uri "InteractionSet" version)) |
| 2081 | (sha256 |
| 2082 | (base32 |
| 2083 | "1nsivm9j0mzkfhwqsa2y9gxxdbaplg4z8vn5dfvls3nrihnqpk4v")))) |
| 2084 | (properties |
| 2085 | `((upstream-name . "InteractionSet"))) |
| 2086 | (build-system r-build-system) |
| 2087 | (propagated-inputs |
| 2088 | `(("r-biocgenerics" ,r-biocgenerics) |
| 2089 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2090 | ("r-genomicranges" ,r-genomicranges) |
| 2091 | ("r-iranges" ,r-iranges) |
| 2092 | ("r-matrix" ,r-matrix) |
| 2093 | ("r-rcpp" ,r-rcpp) |
| 2094 | ("r-s4vectors" ,r-s4vectors) |
| 2095 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 2096 | (native-inputs |
| 2097 | `(("r-knitr" ,r-knitr))) |
| 2098 | (home-page "https://bioconductor.org/packages/InteractionSet") |
| 2099 | (synopsis "Base classes for storing genomic interaction data") |
| 2100 | (description |
| 2101 | "This package provides the @code{GInteractions}, |
| 2102 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
| 2103 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET |
| 2104 | experiments.") |
| 2105 | (license license:gpl3))) |
| 2106 | |
| 2107 | (define-public r-genomicinteractions |
| 2108 | (package |
| 2109 | (name "r-genomicinteractions") |
| 2110 | (version "1.22.0") |
| 2111 | (source |
| 2112 | (origin |
| 2113 | (method url-fetch) |
| 2114 | (uri (bioconductor-uri "GenomicInteractions" version)) |
| 2115 | (sha256 |
| 2116 | (base32 |
| 2117 | "0fg66v31nfajb40da6gxpigm2z11ywkdijs7npvc1mr62ynx9qmy")))) |
| 2118 | (properties |
| 2119 | `((upstream-name . "GenomicInteractions"))) |
| 2120 | (build-system r-build-system) |
| 2121 | (propagated-inputs |
| 2122 | `(("r-biobase" ,r-biobase) |
| 2123 | ("r-biocgenerics" ,r-biocgenerics) |
| 2124 | ("r-data-table" ,r-data-table) |
| 2125 | ("r-dplyr" ,r-dplyr) |
| 2126 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2127 | ("r-genomicranges" ,r-genomicranges) |
| 2128 | ("r-ggplot2" ,r-ggplot2) |
| 2129 | ("r-gridextra" ,r-gridextra) |
| 2130 | ("r-gviz" ,r-gviz) |
| 2131 | ("r-igraph" ,r-igraph) |
| 2132 | ("r-interactionset" ,r-interactionset) |
| 2133 | ("r-iranges" ,r-iranges) |
| 2134 | ("r-rsamtools" ,r-rsamtools) |
| 2135 | ("r-rtracklayer" ,r-rtracklayer) |
| 2136 | ("r-s4vectors" ,r-s4vectors) |
| 2137 | ("r-stringr" ,r-stringr))) |
| 2138 | (native-inputs |
| 2139 | `(("r-knitr" ,r-knitr))) |
| 2140 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") |
| 2141 | (synopsis "R package for handling genomic interaction data") |
| 2142 | (description |
| 2143 | "This R package provides tools for handling genomic interaction data, |
| 2144 | such as ChIA-PET/Hi-C, annotating genomic features with interaction |
| 2145 | information and producing various plots and statistics.") |
| 2146 | (license license:gpl3))) |
| 2147 | |
| 2148 | (define-public r-ctc |
| 2149 | (package |
| 2150 | (name "r-ctc") |
| 2151 | (version "1.62.0") |
| 2152 | (source |
| 2153 | (origin |
| 2154 | (method url-fetch) |
| 2155 | (uri (bioconductor-uri "ctc" version)) |
| 2156 | (sha256 |
| 2157 | (base32 |
| 2158 | "0lv126xj092hps3f3dsv7hasdyy26wcx8npl9idq2l4h9addk6v6")))) |
| 2159 | (build-system r-build-system) |
| 2160 | (propagated-inputs `(("r-amap" ,r-amap))) |
| 2161 | (home-page "https://bioconductor.org/packages/ctc/") |
| 2162 | (synopsis "Cluster and tree conversion") |
| 2163 | (description |
| 2164 | "This package provides tools for exporting and importing classification |
| 2165 | trees and clusters to other programs.") |
| 2166 | (license license:gpl2))) |
| 2167 | |
| 2168 | (define-public r-goseq |
| 2169 | (package |
| 2170 | (name "r-goseq") |
| 2171 | (version "1.40.0") |
| 2172 | (source |
| 2173 | (origin |
| 2174 | (method url-fetch) |
| 2175 | (uri (bioconductor-uri "goseq" version)) |
| 2176 | (sha256 |
| 2177 | (base32 |
| 2178 | "1iyri4rrchzsn8p6wjxr4k30d3cqx3km5mnd9hkfm5d0s7fjzlym")))) |
| 2179 | (build-system r-build-system) |
| 2180 | (propagated-inputs |
| 2181 | `(("r-annotationdbi" ,r-annotationdbi) |
| 2182 | ("r-biasedurn" ,r-biasedurn) |
| 2183 | ("r-biocgenerics" ,r-biocgenerics) |
| 2184 | ("r-genelendatabase" ,r-genelendatabase) |
| 2185 | ("r-go-db" ,r-go-db) |
| 2186 | ("r-mgcv" ,r-mgcv))) |
| 2187 | (home-page "https://bioconductor.org/packages/goseq/") |
| 2188 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") |
| 2189 | (description |
| 2190 | "This package provides tools to detect Gene Ontology and/or other user |
| 2191 | defined categories which are over/under represented in RNA-seq data.") |
| 2192 | (license license:lgpl2.0+))) |
| 2193 | |
| 2194 | (define-public r-glimma |
| 2195 | (package |
| 2196 | (name "r-glimma") |
| 2197 | (version "1.16.0") |
| 2198 | (source |
| 2199 | (origin |
| 2200 | (method url-fetch) |
| 2201 | (uri (bioconductor-uri "Glimma" version)) |
| 2202 | (sha256 |
| 2203 | (base32 |
| 2204 | "1bxfgwjqb9p400a5a5q6p17kcnl3ddz090llihkfih9kyxii9n4y")))) |
| 2205 | (properties `((upstream-name . "Glimma"))) |
| 2206 | (build-system r-build-system) |
| 2207 | (propagated-inputs |
| 2208 | `(("r-edger" ,r-edger) |
| 2209 | ("r-jsonlite" ,r-jsonlite) |
| 2210 | ("r-s4vectors" ,r-s4vectors))) |
| 2211 | (native-inputs |
| 2212 | `(("r-knitr" ,r-knitr))) |
| 2213 | (home-page "https://github.com/Shians/Glimma") |
| 2214 | (synopsis "Interactive HTML graphics") |
| 2215 | (description |
| 2216 | "This package generates interactive visualisations for analysis of |
| 2217 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an |
| 2218 | HTML page. The interactions are built on top of the popular static |
| 2219 | representations of analysis results in order to provide additional |
| 2220 | information.") |
| 2221 | (license license:lgpl3))) |
| 2222 | |
| 2223 | (define-public r-rots |
| 2224 | (package |
| 2225 | (name "r-rots") |
| 2226 | (version "1.16.0") |
| 2227 | (source |
| 2228 | (origin |
| 2229 | (method url-fetch) |
| 2230 | (uri (bioconductor-uri "ROTS" version)) |
| 2231 | (sha256 |
| 2232 | (base32 |
| 2233 | "1mqhi1rfiw7mhiyify7vm3w17p7sc76wjda3ak6690hrc3gsm3cm")))) |
| 2234 | (properties `((upstream-name . "ROTS"))) |
| 2235 | (build-system r-build-system) |
| 2236 | (propagated-inputs |
| 2237 | `(("r-biobase" ,r-biobase) |
| 2238 | ("r-rcpp" ,r-rcpp))) |
| 2239 | (home-page "https://bioconductor.org/packages/ROTS/") |
| 2240 | (synopsis "Reproducibility-Optimized Test Statistic") |
| 2241 | (description |
| 2242 | "This package provides tools for calculating the |
| 2243 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing |
| 2244 | in omics data.") |
| 2245 | (license license:gpl2+))) |
| 2246 | |
| 2247 | (define-public r-plgem |
| 2248 | (package |
| 2249 | (name "r-plgem") |
| 2250 | (version "1.60.0") |
| 2251 | (source |
| 2252 | (origin |
| 2253 | (method url-fetch) |
| 2254 | (uri (bioconductor-uri "plgem" version)) |
| 2255 | (sha256 |
| 2256 | (base32 |
| 2257 | "1fs5nbjnrm7x23y7d9krq56r1kzxka40ca1rs6sq70mn6syhj90a")))) |
| 2258 | (build-system r-build-system) |
| 2259 | (propagated-inputs |
| 2260 | `(("r-biobase" ,r-biobase) |
| 2261 | ("r-mass" ,r-mass))) |
| 2262 | (home-page "http://www.genopolis.it") |
| 2263 | (synopsis "Detect differential expression in microarray and proteomics datasets") |
| 2264 | (description |
| 2265 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully |
| 2266 | model the variance-versus-mean dependence that exists in a variety of |
| 2267 | genome-wide datasets, including microarray and proteomics data. The use of |
| 2268 | PLGEM has been shown to improve the detection of differentially expressed |
| 2269 | genes or proteins in these datasets.") |
| 2270 | (license license:gpl2))) |
| 2271 | |
| 2272 | (define-public r-inspect |
| 2273 | (package |
| 2274 | (name "r-inspect") |
| 2275 | (version "1.18.0") |
| 2276 | (source |
| 2277 | (origin |
| 2278 | (method url-fetch) |
| 2279 | (uri (bioconductor-uri "INSPEcT" version)) |
| 2280 | (sha256 |
| 2281 | (base32 |
| 2282 | "1yyglkdc3ww2jzswhcxk9g1imydfm39krl87as5l9fbm7mv3vd4z")))) |
| 2283 | (properties `((upstream-name . "INSPEcT"))) |
| 2284 | (build-system r-build-system) |
| 2285 | (propagated-inputs |
| 2286 | `(("r-biobase" ,r-biobase) |
| 2287 | ("r-biocgenerics" ,r-biocgenerics) |
| 2288 | ("r-biocparallel" ,r-biocparallel) |
| 2289 | ("r-deseq2" ,r-deseq2) |
| 2290 | ("r-desolve" ,r-desolve) |
| 2291 | ("r-gdata" ,r-gdata) |
| 2292 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2293 | ("r-genomicalignments" ,r-genomicalignments) |
| 2294 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 2295 | ("r-genomicranges" ,r-genomicranges) |
| 2296 | ("r-iranges" ,r-iranges) |
| 2297 | ("r-kernsmooth" ,r-kernsmooth) |
| 2298 | ("r-plgem" ,r-plgem) |
| 2299 | ("r-proc" ,r-proc) |
| 2300 | ("r-rootsolve" ,r-rootsolve) |
| 2301 | ("r-rsamtools" ,r-rsamtools) |
| 2302 | ("r-rtracklayer" ,r-rtracklayer) |
| 2303 | ("r-s4vectors" ,r-s4vectors) |
| 2304 | ("r-shiny" ,r-shiny) |
| 2305 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 2306 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" |
| 2307 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) |
| 2308 | (native-inputs |
| 2309 | `(("r-knitr" ,r-knitr))) |
| 2310 | (home-page "https://bioconductor.org/packages/INSPEcT") |
| 2311 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") |
| 2312 | (description |
| 2313 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in |
| 2314 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in |
| 2315 | order to evaluate synthesis, processing and degradation rates and assess via |
| 2316 | modeling the rates that determines changes in mature mRNA levels.") |
| 2317 | (license license:gpl2))) |
| 2318 | |
| 2319 | (define-public r-dnabarcodes |
| 2320 | (package |
| 2321 | (name "r-dnabarcodes") |
| 2322 | (version "1.18.0") |
| 2323 | (source |
| 2324 | (origin |
| 2325 | (method url-fetch) |
| 2326 | (uri (bioconductor-uri "DNABarcodes" version)) |
| 2327 | (sha256 |
| 2328 | (base32 |
| 2329 | "03y39hjpkb05fnawy3k797bph1iydi1blmpgyy4244zjgk6rs5x7")))) |
| 2330 | (properties `((upstream-name . "DNABarcodes"))) |
| 2331 | (build-system r-build-system) |
| 2332 | (propagated-inputs |
| 2333 | `(("r-bh" ,r-bh) |
| 2334 | ("r-matrix" ,r-matrix) |
| 2335 | ("r-rcpp" ,r-rcpp))) |
| 2336 | (native-inputs |
| 2337 | `(("r-knitr" ,r-knitr))) |
| 2338 | (home-page "https://bioconductor.org/packages/DNABarcodes") |
| 2339 | (synopsis "Create and analyze DNA barcodes") |
| 2340 | (description |
| 2341 | "This package offers tools to create DNA barcode sets capable of |
| 2342 | correcting insertion, deletion, and substitution errors. Existing barcodes |
| 2343 | can be analyzed regarding their minimal, maximal and average distances between |
| 2344 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be |
| 2345 | demultiplexed, i.e. assigned to their original reference barcode.") |
| 2346 | (license license:gpl2))) |
| 2347 | |
| 2348 | (define-public r-ruvseq |
| 2349 | (package |
| 2350 | (name "r-ruvseq") |
| 2351 | (version "1.22.0") |
| 2352 | (source |
| 2353 | (origin |
| 2354 | (method url-fetch) |
| 2355 | (uri (bioconductor-uri "RUVSeq" version)) |
| 2356 | (sha256 |
| 2357 | (base32 |
| 2358 | "0yqs9xgyzw3cwb4l7zjl1cjgbsjp05qrqnwyvh7q81wdp7x5p55x")))) |
| 2359 | (properties `((upstream-name . "RUVSeq"))) |
| 2360 | (build-system r-build-system) |
| 2361 | (propagated-inputs |
| 2362 | `(("r-biobase" ,r-biobase) |
| 2363 | ("r-edaseq" ,r-edaseq) |
| 2364 | ("r-edger" ,r-edger) |
| 2365 | ("r-mass" ,r-mass))) |
| 2366 | (native-inputs |
| 2367 | `(("r-knitr" ,r-knitr))) |
| 2368 | (home-page "https://github.com/drisso/RUVSeq") |
| 2369 | (synopsis "Remove unwanted variation from RNA-Seq data") |
| 2370 | (description |
| 2371 | "This package implements methods to @dfn{remove unwanted variation} (RUV) |
| 2372 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between |
| 2373 | samples.") |
| 2374 | (license license:artistic2.0))) |
| 2375 | |
| 2376 | (define-public r-biocneighbors |
| 2377 | (package |
| 2378 | (name "r-biocneighbors") |
| 2379 | (version "1.6.0") |
| 2380 | (source |
| 2381 | (origin |
| 2382 | (method url-fetch) |
| 2383 | (uri (bioconductor-uri "BiocNeighbors" version)) |
| 2384 | (sha256 |
| 2385 | (base32 |
| 2386 | "14cyyrwxi82xm5wy6bb1176zg322ll67wjrw9vvi4fhfs1k4wqxy")))) |
| 2387 | (properties `((upstream-name . "BiocNeighbors"))) |
| 2388 | (build-system r-build-system) |
| 2389 | (propagated-inputs |
| 2390 | `(("r-biocparallel" ,r-biocparallel) |
| 2391 | ("r-matrix" ,r-matrix) |
| 2392 | ("r-rcpp" ,r-rcpp) |
| 2393 | ("r-rcppannoy" ,r-rcppannoy) |
| 2394 | ("r-rcpphnsw" ,r-rcpphnsw) |
| 2395 | ("r-s4vectors" ,r-s4vectors))) |
| 2396 | (native-inputs |
| 2397 | `(("r-knitr" ,r-knitr))) |
| 2398 | (home-page "https://bioconductor.org/packages/BiocNeighbors") |
| 2399 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") |
| 2400 | (description |
| 2401 | "This package implements exact and approximate methods for nearest |
| 2402 | neighbor detection, in a framework that allows them to be easily switched |
| 2403 | within Bioconductor packages or workflows. The exact algorithm is implemented |
| 2404 | using pre-clustering with the k-means algorithm. Functions are also provided |
| 2405 | to search for all neighbors within a given distance. Parallelization is |
| 2406 | achieved for all methods using the BiocParallel framework.") |
| 2407 | (license license:gpl3))) |
| 2408 | |
| 2409 | (define-public r-biocsingular |
| 2410 | (package |
| 2411 | (name "r-biocsingular") |
| 2412 | (version "1.4.0") |
| 2413 | (source |
| 2414 | (origin |
| 2415 | (method url-fetch) |
| 2416 | (uri (bioconductor-uri "BiocSingular" version)) |
| 2417 | (sha256 |
| 2418 | (base32 |
| 2419 | "0368a9xj4cvicqkxmhh12ln46q9gnxla70s1dqrxxfn3b6k525ih")))) |
| 2420 | (properties `((upstream-name . "BiocSingular"))) |
| 2421 | (build-system r-build-system) |
| 2422 | (propagated-inputs |
| 2423 | `(("r-beachmat" ,r-beachmat) |
| 2424 | ("r-biocgenerics" ,r-biocgenerics) |
| 2425 | ("r-biocparallel" ,r-biocparallel) |
| 2426 | ("r-delayedarray" ,r-delayedarray) |
| 2427 | ("r-irlba" ,r-irlba) |
| 2428 | ("r-matrix" ,r-matrix) |
| 2429 | ("r-rcpp" ,r-rcpp) |
| 2430 | ("r-rsvd" ,r-rsvd) |
| 2431 | ("r-s4vectors" ,r-s4vectors))) |
| 2432 | (native-inputs |
| 2433 | `(("r-knitr" ,r-knitr))) |
| 2434 | (home-page "https://github.com/LTLA/BiocSingular") |
| 2435 | (synopsis "Singular value decomposition for Bioconductor packages") |
| 2436 | (description |
| 2437 | "This package implements exact and approximate methods for singular value |
| 2438 | decomposition and principal components analysis, in a framework that allows |
| 2439 | them to be easily switched within Bioconductor packages or workflows. Where |
| 2440 | possible, parallelization is achieved using the BiocParallel framework.") |
| 2441 | (license license:gpl3))) |
| 2442 | |
| 2443 | (define-public r-destiny |
| 2444 | (package |
| 2445 | (name "r-destiny") |
| 2446 | (version "3.2.0") |
| 2447 | (source |
| 2448 | (origin |
| 2449 | (method url-fetch) |
| 2450 | (uri (bioconductor-uri "destiny" version)) |
| 2451 | (sha256 |
| 2452 | (base32 |
| 2453 | "0ik5vwxz9cci3glwgb5ff03sfyr4sjcp8ckfymlgmlm6fz8cp21n")))) |
| 2454 | (build-system r-build-system) |
| 2455 | (propagated-inputs |
| 2456 | `(("r-biobase" ,r-biobase) |
| 2457 | ("r-biocgenerics" ,r-biocgenerics) |
| 2458 | ("r-ggplot-multistats" ,r-ggplot-multistats) |
| 2459 | ("r-ggplot2" ,r-ggplot2) |
| 2460 | ("r-ggthemes" ,r-ggthemes) |
| 2461 | ("r-irlba" ,r-irlba) |
| 2462 | ("r-knn-covertree" ,r-knn-covertree) |
| 2463 | ("r-matrix" ,r-matrix) |
| 2464 | ("r-nbconvertr" ,r-nbconvertr) |
| 2465 | ("r-pcamethods" ,r-pcamethods) |
| 2466 | ("r-proxy" ,r-proxy) |
| 2467 | ("r-rcpp" ,r-rcpp) |
| 2468 | ("r-rcppeigen" ,r-rcppeigen) |
| 2469 | ("r-rcpphnsw" ,r-rcpphnsw) |
| 2470 | ("r-rspectra" ,r-rspectra) |
| 2471 | ("r-scales" ,r-scales) |
| 2472 | ("r-scatterplot3d" ,r-scatterplot3d) |
| 2473 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
| 2474 | ("r-smoother" ,r-smoother) |
| 2475 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 2476 | ("r-tidyr" ,r-tidyr) |
| 2477 | ("r-tidyselect" ,r-tidyselect) |
| 2478 | ("r-vim" ,r-vim))) |
| 2479 | (native-inputs |
| 2480 | `(("r-nbconvertr" ,r-nbconvertr))) ; for vignettes |
| 2481 | (home-page "https://bioconductor.org/packages/destiny/") |
| 2482 | (synopsis "Create and plot diffusion maps") |
| 2483 | (description "This package provides tools to create and plot diffusion |
| 2484 | maps.") |
| 2485 | ;; Any version of the GPL |
| 2486 | (license license:gpl3+))) |
| 2487 | |
| 2488 | (define-public r-savr |
| 2489 | (package |
| 2490 | (name "r-savr") |
| 2491 | (version "1.26.0") |
| 2492 | (source |
| 2493 | (origin |
| 2494 | (method url-fetch) |
| 2495 | (uri (bioconductor-uri "savR" version)) |
| 2496 | (sha256 |
| 2497 | (base32 |
| 2498 | "17jdnr47ivblfspr4b32z9fds1fqiiwsi2z6r524g1v4944p8w5a")))) |
| 2499 | (properties `((upstream-name . "savR"))) |
| 2500 | (build-system r-build-system) |
| 2501 | (propagated-inputs |
| 2502 | `(("r-ggplot2" ,r-ggplot2) |
| 2503 | ("r-gridextra" ,r-gridextra) |
| 2504 | ("r-reshape2" ,r-reshape2) |
| 2505 | ("r-scales" ,r-scales) |
| 2506 | ("r-xml" ,r-xml))) |
| 2507 | (home-page "https://github.com/bcalder/savR") |
| 2508 | (synopsis "Parse and analyze Illumina SAV files") |
| 2509 | (description |
| 2510 | "This package provides tools to parse Illumina Sequence Analysis |
| 2511 | Viewer (SAV) files, access data, and generate QC plots.") |
| 2512 | (license license:agpl3+))) |
| 2513 | |
| 2514 | (define-public r-chipexoqual |
| 2515 | (package |
| 2516 | (name "r-chipexoqual") |
| 2517 | (version "1.10.0") |
| 2518 | (source |
| 2519 | (origin |
| 2520 | (method url-fetch) |
| 2521 | (uri (bioconductor-uri "ChIPexoQual" version)) |
| 2522 | (sha256 |
| 2523 | (base32 |
| 2524 | "044n6kn16qczpdhp0w0z5x8xpr0rfs9s8q70rafgnvj7a2q1xdd0")))) |
| 2525 | (properties `((upstream-name . "ChIPexoQual"))) |
| 2526 | (build-system r-build-system) |
| 2527 | (propagated-inputs |
| 2528 | `(("r-biocparallel" ,r-biocparallel) |
| 2529 | ("r-biovizbase" ,r-biovizbase) |
| 2530 | ("r-broom" ,r-broom) |
| 2531 | ("r-data-table" ,r-data-table) |
| 2532 | ("r-dplyr" ,r-dplyr) |
| 2533 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2534 | ("r-genomicalignments" ,r-genomicalignments) |
| 2535 | ("r-genomicranges" ,r-genomicranges) |
| 2536 | ("r-ggplot2" ,r-ggplot2) |
| 2537 | ("r-hexbin" ,r-hexbin) |
| 2538 | ("r-iranges" ,r-iranges) |
| 2539 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 2540 | ("r-rmarkdown" ,r-rmarkdown) |
| 2541 | ("r-rsamtools" ,r-rsamtools) |
| 2542 | ("r-s4vectors" ,r-s4vectors) |
| 2543 | ("r-scales" ,r-scales) |
| 2544 | ("r-viridis" ,r-viridis))) |
| 2545 | (home-page "https://github.com/keleslab/ChIPexoQual") |
| 2546 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") |
| 2547 | (description |
| 2548 | "This package provides a quality control pipeline for ChIP-exo/nexus |
| 2549 | sequencing data.") |
| 2550 | (license license:gpl2+))) |
| 2551 | |
| 2552 | (define-public r-copynumber |
| 2553 | (package |
| 2554 | (name "r-copynumber") |
| 2555 | (version "1.26.0") |
| 2556 | (source (origin |
| 2557 | (method url-fetch) |
| 2558 | (uri (bioconductor-uri "copynumber" version)) |
| 2559 | (sha256 |
| 2560 | (base32 |
| 2561 | "0r6r1adj20x3ckm0dlipxlf1rzngr92xsxxpy81mqxf4jpmyr8gj")))) |
| 2562 | (build-system r-build-system) |
| 2563 | (propagated-inputs |
| 2564 | `(("r-s4vectors" ,r-s4vectors) |
| 2565 | ("r-iranges" ,r-iranges) |
| 2566 | ("r-genomicranges" ,r-genomicranges) |
| 2567 | ("r-biocgenerics" ,r-biocgenerics))) |
| 2568 | (home-page "https://bioconductor.org/packages/copynumber") |
| 2569 | (synopsis "Segmentation of single- and multi-track copy number data") |
| 2570 | (description |
| 2571 | "This package segments single- and multi-track copy number data by a |
| 2572 | penalized least squares regression method.") |
| 2573 | (license license:artistic2.0))) |
| 2574 | |
| 2575 | (define-public r-dnacopy |
| 2576 | (package |
| 2577 | (name "r-dnacopy") |
| 2578 | (version "1.60.0") |
| 2579 | (source |
| 2580 | (origin |
| 2581 | (method url-fetch) |
| 2582 | (uri (bioconductor-uri "DNAcopy" version)) |
| 2583 | (sha256 |
| 2584 | (base32 |
| 2585 | "119z5lqhhw9ppg6s4dvbxk1kxf3wc55ibpm9b88c91s04yd7m9yw")))) |
| 2586 | (properties `((upstream-name . "DNAcopy"))) |
| 2587 | (build-system r-build-system) |
| 2588 | (native-inputs `(("gfortran" ,gfortran))) |
| 2589 | (home-page "https://bioconductor.org/packages/DNAcopy") |
| 2590 | (synopsis "DNA copy number data analysis") |
| 2591 | (description |
| 2592 | "This package implements the @dfn{circular binary segmentation} (CBS) |
| 2593 | algorithm to segment DNA copy number data and identify genomic regions with |
| 2594 | abnormal copy number.") |
| 2595 | (license license:gpl2+))) |
| 2596 | |
| 2597 | ;; This is a CRAN package, but it uncharacteristically depends on a |
| 2598 | ;; Bioconductor package. |
| 2599 | (define-public r-htscluster |
| 2600 | (package |
| 2601 | (name "r-htscluster") |
| 2602 | (version "2.0.8") |
| 2603 | (source |
| 2604 | (origin |
| 2605 | (method url-fetch) |
| 2606 | (uri (cran-uri "HTSCluster" version)) |
| 2607 | (sha256 |
| 2608 | (base32 |
| 2609 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) |
| 2610 | (properties `((upstream-name . "HTSCluster"))) |
| 2611 | (build-system r-build-system) |
| 2612 | (propagated-inputs |
| 2613 | `(("r-capushe" ,r-capushe) |
| 2614 | ("r-edger" ,r-edger) |
| 2615 | ("r-plotrix" ,r-plotrix))) |
| 2616 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") |
| 2617 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") |
| 2618 | (description |
| 2619 | "This package provides a Poisson mixture model is implemented to cluster |
| 2620 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter |
| 2621 | estimation is performed using either the EM or CEM algorithm, and the slope |
| 2622 | heuristics are used for model selection (i.e., to choose the number of |
| 2623 | clusters).") |
| 2624 | (license license:gpl3+))) |
| 2625 | |
| 2626 | (define-public r-deds |
| 2627 | (package |
| 2628 | (name "r-deds") |
| 2629 | (version "1.60.0") |
| 2630 | (source |
| 2631 | (origin |
| 2632 | (method url-fetch) |
| 2633 | (uri (bioconductor-uri "DEDS" version)) |
| 2634 | (sha256 |
| 2635 | (base32 |
| 2636 | "0vzsmah2lhxf8k6n4d0i4j609sbvygmb6ii2ridg9z3nskwkrhp8")))) |
| 2637 | (properties `((upstream-name . "DEDS"))) |
| 2638 | (build-system r-build-system) |
| 2639 | (home-page "https://bioconductor.org/packages/DEDS/") |
| 2640 | (synopsis "Differential expression via distance summary for microarray data") |
| 2641 | (description |
| 2642 | "This library contains functions that calculate various statistics of |
| 2643 | differential expression for microarray data, including t statistics, fold |
| 2644 | change, F statistics, SAM, moderated t and F statistics and B statistics. It |
| 2645 | also implements a new methodology called DEDS (Differential Expression via |
| 2646 | Distance Summary), which selects differentially expressed genes by integrating |
| 2647 | and summarizing a set of statistics using a weighted distance approach.") |
| 2648 | ;; Any version of the LGPL. |
| 2649 | (license license:lgpl3+))) |
| 2650 | |
| 2651 | ;; This is a CRAN package, but since it depends on a Bioconductor package we |
| 2652 | ;; put it here. |
| 2653 | (define-public r-nbpseq |
| 2654 | (package |
| 2655 | (name "r-nbpseq") |
| 2656 | (version "0.3.0") |
| 2657 | (source |
| 2658 | (origin |
| 2659 | (method url-fetch) |
| 2660 | (uri (cran-uri "NBPSeq" version)) |
| 2661 | (sha256 |
| 2662 | (base32 |
| 2663 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) |
| 2664 | (properties `((upstream-name . "NBPSeq"))) |
| 2665 | (build-system r-build-system) |
| 2666 | (propagated-inputs |
| 2667 | `(("r-qvalue" ,r-qvalue))) |
| 2668 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") |
| 2669 | (synopsis "Negative binomial models for RNA-Seq data") |
| 2670 | (description |
| 2671 | "This package provides negative binomial models for two-group comparisons |
| 2672 | and regression inferences from RNA-sequencing data.") |
| 2673 | (license license:gpl2))) |
| 2674 | |
| 2675 | (define-public r-ebseq |
| 2676 | (package |
| 2677 | (name "r-ebseq") |
| 2678 | (version "1.26.0") |
| 2679 | (source |
| 2680 | (origin |
| 2681 | (method url-fetch) |
| 2682 | (uri (bioconductor-uri "EBSeq" version)) |
| 2683 | (sha256 |
| 2684 | (base32 |
| 2685 | "0ay1vcccpc29r3vinlnwp9256345bfb346kg2y11kib4bnrabjb6")))) |
| 2686 | (properties `((upstream-name . "EBSeq"))) |
| 2687 | (build-system r-build-system) |
| 2688 | (propagated-inputs |
| 2689 | `(("r-blockmodeling" ,r-blockmodeling) |
| 2690 | ("r-gplots" ,r-gplots) |
| 2691 | ("r-testthat" ,r-testthat))) |
| 2692 | (home-page "https://bioconductor.org/packages/EBSeq") |
| 2693 | (synopsis "Differential expression analysis of RNA-seq data") |
| 2694 | (description |
| 2695 | "This package provides tools for differential expression analysis at both |
| 2696 | gene and isoform level using RNA-seq data") |
| 2697 | (license license:artistic2.0))) |
| 2698 | |
| 2699 | (define-public r-karyoploter |
| 2700 | (package |
| 2701 | (name "r-karyoploter") |
| 2702 | (version "1.12.4") |
| 2703 | (source (origin |
| 2704 | (method url-fetch) |
| 2705 | (uri (bioconductor-uri "karyoploteR" version)) |
| 2706 | (sha256 |
| 2707 | (base32 |
| 2708 | "03jmfgmw35hrgn3pc5lq6pblzhfx9fp4l6dx50rp303lr7kjxp9v")))) |
| 2709 | (build-system r-build-system) |
| 2710 | (propagated-inputs |
| 2711 | `(("r-regioner" ,r-regioner) |
| 2712 | ("r-genomicranges" ,r-genomicranges) |
| 2713 | ("r-iranges" ,r-iranges) |
| 2714 | ("r-rsamtools" ,r-rsamtools) |
| 2715 | ("r-memoise" ,r-memoise) |
| 2716 | ("r-rtracklayer" ,r-rtracklayer) |
| 2717 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2718 | ("r-s4vectors" ,r-s4vectors) |
| 2719 | ("r-biovizbase" ,r-biovizbase) |
| 2720 | ("r-digest" ,r-digest) |
| 2721 | ("r-bezier" ,r-bezier) |
| 2722 | ("r-bamsignals" ,r-bamsignals) |
| 2723 | ("r-annotationdbi" ,r-annotationdbi) |
| 2724 | ("r-variantannotation" ,r-variantannotation))) |
| 2725 | (home-page "https://bioconductor.org/packages/karyoploteR/") |
| 2726 | (synopsis "Plot customizable linear genomes displaying arbitrary data") |
| 2727 | (description "This package creates karyotype plots of arbitrary genomes and |
| 2728 | offers a complete set of functions to plot arbitrary data on them. It mimicks |
| 2729 | many R base graphics functions coupling them with a coordinate change function |
| 2730 | automatically mapping the chromosome and data coordinates into the plot |
| 2731 | coordinates.") |
| 2732 | (license license:artistic2.0))) |
| 2733 | |
| 2734 | (define-public r-lpsymphony |
| 2735 | (package |
| 2736 | (name "r-lpsymphony") |
| 2737 | (version "1.14.0") |
| 2738 | (source |
| 2739 | (origin |
| 2740 | (method url-fetch) |
| 2741 | (uri (bioconductor-uri "lpsymphony" version)) |
| 2742 | (sha256 |
| 2743 | (base32 |
| 2744 | "0j5j9kggh3l61vp6hpnqf45d5kzifksaj0sqhvs1zahmx2c1gfdv")))) |
| 2745 | (build-system r-build-system) |
| 2746 | (inputs |
| 2747 | `(("gfortran" ,gfortran) |
| 2748 | ("zlib" ,zlib))) |
| 2749 | (native-inputs |
| 2750 | `(("pkg-config" ,pkg-config))) |
| 2751 | (home-page "https://r-forge.r-project.org/projects/rsymphony") |
| 2752 | (synopsis "Symphony integer linear programming solver in R") |
| 2753 | (description |
| 2754 | "This package was derived from Rsymphony. The package provides an R |
| 2755 | interface to SYMPHONY, a linear programming solver written in C++. The main |
| 2756 | difference between this package and Rsymphony is that it includes the solver |
| 2757 | source code, while Rsymphony expects to find header and library files on the |
| 2758 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy |
| 2759 | to install interface to SYMPHONY.") |
| 2760 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. |
| 2761 | ;; lpsimphony is released under the same terms. |
| 2762 | (license license:epl1.0))) |
| 2763 | |
| 2764 | (define-public r-ihw |
| 2765 | (package |
| 2766 | (name "r-ihw") |
| 2767 | (version "1.14.0") |
| 2768 | (source |
| 2769 | (origin |
| 2770 | (method url-fetch) |
| 2771 | (uri (bioconductor-uri "IHW" version)) |
| 2772 | (sha256 |
| 2773 | (base32 |
| 2774 | "0rnw7r9pylpj3a5graavcpiqv2v67rv2a4dlcynkf4ihpxs4bg8x")))) |
| 2775 | (properties `((upstream-name . "IHW"))) |
| 2776 | (build-system r-build-system) |
| 2777 | (propagated-inputs |
| 2778 | `(("r-biocgenerics" ,r-biocgenerics) |
| 2779 | ("r-fdrtool" ,r-fdrtool) |
| 2780 | ("r-lpsymphony" ,r-lpsymphony) |
| 2781 | ("r-slam" ,r-slam))) |
| 2782 | (home-page "https://bioconductor.org/packages/IHW") |
| 2783 | (synopsis "Independent hypothesis weighting") |
| 2784 | (description |
| 2785 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing |
| 2786 | procedure that increases power compared to the method of Benjamini and |
| 2787 | Hochberg by assigning data-driven weights to each hypothesis. The input to |
| 2788 | IHW is a two-column table of p-values and covariates. The covariate can be |
| 2789 | any continuous-valued or categorical variable that is thought to be |
| 2790 | informative on the statistical properties of each hypothesis test, while it is |
| 2791 | independent of the p-value under the null hypothesis.") |
| 2792 | (license license:artistic2.0))) |
| 2793 | |
| 2794 | (define-public r-icobra |
| 2795 | (package |
| 2796 | (name "r-icobra") |
| 2797 | (version "1.14.0") |
| 2798 | (source |
| 2799 | (origin |
| 2800 | (method url-fetch) |
| 2801 | (uri (bioconductor-uri "iCOBRA" version)) |
| 2802 | (sha256 |
| 2803 | (base32 |
| 2804 | "1l0yr2grpwmr3pc5h50p1j4nxyb1ddmc55l7rhxpp4igh4fq1avz")))) |
| 2805 | (properties `((upstream-name . "iCOBRA"))) |
| 2806 | (build-system r-build-system) |
| 2807 | (propagated-inputs |
| 2808 | `(("r-dplyr" ,r-dplyr) |
| 2809 | ("r-dt" ,r-dt) |
| 2810 | ("r-ggplot2" ,r-ggplot2) |
| 2811 | ("r-limma" ,r-limma) |
| 2812 | ("r-reshape2" ,r-reshape2) |
| 2813 | ("r-rocr" ,r-rocr) |
| 2814 | ("r-scales" ,r-scales) |
| 2815 | ("r-shiny" ,r-shiny) |
| 2816 | ("r-shinybs" ,r-shinybs) |
| 2817 | ("r-shinydashboard" ,r-shinydashboard) |
| 2818 | ("r-upsetr" ,r-upsetr))) |
| 2819 | (home-page "https://bioconductor.org/packages/iCOBRA") |
| 2820 | (synopsis "Comparison and visualization of ranking and assignment methods") |
| 2821 | (description |
| 2822 | "This package provides functions for calculation and visualization of |
| 2823 | performance metrics for evaluation of ranking and binary |
| 2824 | classification (assignment) methods. It also contains a Shiny application for |
| 2825 | interactive exploration of results.") |
| 2826 | (license license:gpl2+))) |
| 2827 | |
| 2828 | (define-public r-mast |
| 2829 | (package |
| 2830 | (name "r-mast") |
| 2831 | (version "1.12.0") |
| 2832 | (source |
| 2833 | (origin |
| 2834 | (method url-fetch) |
| 2835 | (uri (bioconductor-uri "MAST" version)) |
| 2836 | (sha256 |
| 2837 | (base32 |
| 2838 | "1l78rrwkzyswpj6pgc9z8290fqrk4akba76invkkazpyh91r8gga")))) |
| 2839 | (properties `((upstream-name . "MAST"))) |
| 2840 | (build-system r-build-system) |
| 2841 | (propagated-inputs |
| 2842 | `(("r-abind" ,r-abind) |
| 2843 | ("r-biobase" ,r-biobase) |
| 2844 | ("r-biocgenerics" ,r-biocgenerics) |
| 2845 | ("r-data-table" ,r-data-table) |
| 2846 | ("r-ggplot2" ,r-ggplot2) |
| 2847 | ("r-plyr" ,r-plyr) |
| 2848 | ("r-progress" ,r-progress) |
| 2849 | ("r-reshape2" ,r-reshape2) |
| 2850 | ("r-s4vectors" ,r-s4vectors) |
| 2851 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
| 2852 | ("r-stringr" ,r-stringr) |
| 2853 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 2854 | (native-inputs |
| 2855 | `(("r-knitr" ,r-knitr))) |
| 2856 | (home-page "https://github.com/RGLab/MAST/") |
| 2857 | (synopsis "Model-based analysis of single cell transcriptomics") |
| 2858 | (description |
| 2859 | "This package provides methods and models for handling zero-inflated |
| 2860 | single cell assay data.") |
| 2861 | (license license:gpl2+))) |
| 2862 | |
| 2863 | (define-public r-monocle |
| 2864 | (package |
| 2865 | (name "r-monocle") |
| 2866 | (version "2.14.0") |
| 2867 | (source |
| 2868 | (origin |
| 2869 | (method url-fetch) |
| 2870 | (uri (bioconductor-uri "monocle" version)) |
| 2871 | (sha256 |
| 2872 | (base32 |
| 2873 | "18b9y592q48mbcp5w095qs1kaklq64v6dcnlpqhv3rwxvywygsz2")))) |
| 2874 | (build-system r-build-system) |
| 2875 | (propagated-inputs |
| 2876 | `(("r-biobase" ,r-biobase) |
| 2877 | ("r-biocgenerics" ,r-biocgenerics) |
| 2878 | ("r-biocviews" ,r-biocviews) |
| 2879 | ("r-cluster" ,r-cluster) |
| 2880 | ("r-combinat" ,r-combinat) |
| 2881 | ("r-ddrtree" ,r-ddrtree) |
| 2882 | ("r-densityclust" ,r-densityclust) |
| 2883 | ("r-dplyr" ,r-dplyr) |
| 2884 | ("r-fastica" ,r-fastica) |
| 2885 | ("r-ggplot2" ,r-ggplot2) |
| 2886 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) |
| 2887 | ("r-igraph" ,r-igraph) |
| 2888 | ("r-irlba" ,r-irlba) |
| 2889 | ("r-limma" ,r-limma) |
| 2890 | ("r-mass" ,r-mass) |
| 2891 | ("r-matrix" ,r-matrix) |
| 2892 | ("r-matrixstats" ,r-matrixstats) |
| 2893 | ("r-pheatmap" ,r-pheatmap) |
| 2894 | ("r-plyr" ,r-plyr) |
| 2895 | ("r-proxy" ,r-proxy) |
| 2896 | ("r-qlcmatrix" ,r-qlcmatrix) |
| 2897 | ("r-rann" ,r-rann) |
| 2898 | ("r-rcpp" ,r-rcpp) |
| 2899 | ("r-reshape2" ,r-reshape2) |
| 2900 | ("r-rtsne" ,r-rtsne) |
| 2901 | ("r-slam" ,r-slam) |
| 2902 | ("r-stringr" ,r-stringr) |
| 2903 | ("r-tibble" ,r-tibble) |
| 2904 | ("r-vgam" ,r-vgam) |
| 2905 | ("r-viridis" ,r-viridis))) |
| 2906 | (home-page "https://bioconductor.org/packages/monocle") |
| 2907 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") |
| 2908 | (description |
| 2909 | "Monocle performs differential expression and time-series analysis for |
| 2910 | single-cell expression experiments. It orders individual cells according to |
| 2911 | progress through a biological process, without knowing ahead of time which |
| 2912 | genes define progress through that process. Monocle also performs |
| 2913 | differential expression analysis, clustering, visualization, and other useful |
| 2914 | tasks on single cell expression data. It is designed to work with RNA-Seq and |
| 2915 | qPCR data, but could be used with other types as well.") |
| 2916 | (license license:artistic2.0))) |
| 2917 | |
| 2918 | (define-public r-monocle3 |
| 2919 | (package |
| 2920 | (name "r-monocle3") |
| 2921 | (version "0.1.2") |
| 2922 | (source |
| 2923 | (origin |
| 2924 | (method git-fetch) |
| 2925 | (uri (git-reference |
| 2926 | (url "https://github.com/cole-trapnell-lab/monocle3.git") |
| 2927 | (commit version))) |
| 2928 | (file-name (git-file-name name version)) |
| 2929 | (sha256 |
| 2930 | (base32 |
| 2931 | "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) |
| 2932 | (build-system r-build-system) |
| 2933 | (propagated-inputs |
| 2934 | `(("r-biobase" ,r-biobase) |
| 2935 | ("r-biocgenerics" ,r-biocgenerics) |
| 2936 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) |
| 2937 | ("r-dplyr" ,r-dplyr) |
| 2938 | ("r-ggplot2" ,r-ggplot2) |
| 2939 | ("r-ggrepel" ,r-ggrepel) |
| 2940 | ("r-grr" ,r-grr) |
| 2941 | ("r-htmlwidgets" ,r-htmlwidgets) |
| 2942 | ("r-igraph" ,r-igraph) |
| 2943 | ("r-irlba" ,r-irlba) |
| 2944 | ("r-limma" ,r-limma) |
| 2945 | ("r-lmtest" ,r-lmtest) |
| 2946 | ("r-mass" ,r-mass) |
| 2947 | ("r-matrix" ,r-matrix) |
| 2948 | ("r-matrix-utils" ,r-matrix-utils) |
| 2949 | ("r-pbapply" ,r-pbapply) |
| 2950 | ("r-pbmcapply" ,r-pbmcapply) |
| 2951 | ("r-pheatmap" ,r-pheatmap) |
| 2952 | ("r-plotly" ,r-plotly) |
| 2953 | ("r-pryr" ,r-pryr) |
| 2954 | ("r-proxy" ,r-proxy) |
| 2955 | ("r-pscl" ,r-pscl) |
| 2956 | ("r-purrr" ,r-purrr) |
| 2957 | ("r-rann" ,r-rann) |
| 2958 | ("r-rcpp" ,r-rcpp) |
| 2959 | ("r-rcppparallel" ,r-rcppparallel) |
| 2960 | ("r-reshape2" ,r-reshape2) |
| 2961 | ("r-reticulate" ,r-reticulate) |
| 2962 | ("r-rhpcblasctl" ,r-rhpcblasctl) |
| 2963 | ("r-rtsne" ,r-rtsne) |
| 2964 | ("r-shiny" ,r-shiny) |
| 2965 | ("r-slam" ,r-slam) |
| 2966 | ("r-spdep" ,r-spdep) |
| 2967 | ("r-speedglm" ,r-speedglm) |
| 2968 | ("r-stringr" ,r-stringr) |
| 2969 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
| 2970 | ("r-tibble" ,r-tibble) |
| 2971 | ("r-tidyr" ,r-tidyr) |
| 2972 | ("r-uwot" ,r-uwot) |
| 2973 | ("r-viridis" ,r-viridis))) |
| 2974 | (home-page "https://github.com/cole-trapnell-lab/monocle3") |
| 2975 | (synopsis "Analysis toolkit for single-cell RNA-Seq data") |
| 2976 | (description |
| 2977 | "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") |
| 2978 | (license license:expat))) |
| 2979 | |
| 2980 | (define-public r-noiseq |
| 2981 | (package |
| 2982 | (name "r-noiseq") |
| 2983 | (version "2.30.0") |
| 2984 | (source |
| 2985 | (origin |
| 2986 | (method url-fetch) |
| 2987 | (uri (bioconductor-uri "NOISeq" version)) |
| 2988 | (sha256 |
| 2989 | (base32 |
| 2990 | "1a8p66hhnwmay0rjabwq7356wr93yn33nqgr9rr7whpp9nls1hg4")))) |
| 2991 | (properties `((upstream-name . "NOISeq"))) |
| 2992 | (build-system r-build-system) |
| 2993 | (propagated-inputs |
| 2994 | `(("r-biobase" ,r-biobase) |
| 2995 | ("r-matrix" ,r-matrix))) |
| 2996 | (home-page "https://bioconductor.org/packages/NOISeq") |
| 2997 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") |
| 2998 | (description |
| 2999 | "This package provides tools to support the analysis of RNA-seq |
| 3000 | expression data or other similar kind of data. It provides exploratory plots |
| 3001 | to evaluate saturation, count distribution, expression per chromosome, type of |
| 3002 | detected features, features length, etc. It also supports the analysis of |
| 3003 | differential expression between two experimental conditions with no parametric |
| 3004 | assumptions.") |
| 3005 | (license license:artistic2.0))) |
| 3006 | |
| 3007 | (define-public r-scdd |
| 3008 | (package |
| 3009 | (name "r-scdd") |
| 3010 | (version "1.10.0") |
| 3011 | (source |
| 3012 | (origin |
| 3013 | (method url-fetch) |
| 3014 | (uri (bioconductor-uri "scDD" version)) |
| 3015 | (sha256 |
| 3016 | (base32 |
| 3017 | "0nk0qq664zs7dnlcamdkrrhvll01p7f96jj3igbxxlzj3dvr58w4")))) |
| 3018 | (properties `((upstream-name . "scDD"))) |
| 3019 | (build-system r-build-system) |
| 3020 | (propagated-inputs |
| 3021 | `(("r-arm" ,r-arm) |
| 3022 | ("r-biocparallel" ,r-biocparallel) |
| 3023 | ("r-ebseq" ,r-ebseq) |
| 3024 | ("r-fields" ,r-fields) |
| 3025 | ("r-ggplot2" ,r-ggplot2) |
| 3026 | ("r-mclust" ,r-mclust) |
| 3027 | ("r-outliers" ,r-outliers) |
| 3028 | ("r-s4vectors" ,r-s4vectors) |
| 3029 | ("r-scran" ,r-scran) |
| 3030 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
| 3031 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 3032 | (home-page "https://github.com/kdkorthauer/scDD") |
| 3033 | (synopsis "Mixture modeling of single-cell RNA-seq data") |
| 3034 | (description |
| 3035 | "This package implements a method to analyze single-cell RNA-seq data |
| 3036 | utilizing flexible Dirichlet Process mixture models. Genes with differential |
| 3037 | distributions of expression are classified into several interesting patterns |
| 3038 | of differences between two conditions. The package also includes functions |
| 3039 | for simulating data with these patterns from negative binomial |
| 3040 | distributions.") |
| 3041 | (license license:gpl2))) |
| 3042 | |
| 3043 | (define-public r-scone |
| 3044 | (package |
| 3045 | (name "r-scone") |
| 3046 | (version "1.10.0") |
| 3047 | (source |
| 3048 | (origin |
| 3049 | (method url-fetch) |
| 3050 | (uri (bioconductor-uri "scone" version)) |
| 3051 | (sha256 |
| 3052 | (base32 |
| 3053 | "1hfsbnix0y9ad6bj0d8q2aw13pb3vjcaa0dfwxxapzl90zwbsjhp")))) |
| 3054 | (build-system r-build-system) |
| 3055 | (propagated-inputs |
| 3056 | `(("r-aroma-light" ,r-aroma-light) |
| 3057 | ("r-biocparallel" ,r-biocparallel) |
| 3058 | ("r-boot" ,r-boot) |
| 3059 | ("r-class" ,r-class) |
| 3060 | ("r-cluster" ,r-cluster) |
| 3061 | ("r-compositions" ,r-compositions) |
| 3062 | ("r-diptest" ,r-diptest) |
| 3063 | ("r-edger" ,r-edger) |
| 3064 | ("r-fpc" ,r-fpc) |
| 3065 | ("r-gplots" ,r-gplots) |
| 3066 | ("r-hexbin" ,r-hexbin) |
| 3067 | ("r-limma" ,r-limma) |
| 3068 | ("r-matrixstats" ,r-matrixstats) |
| 3069 | ("r-mixtools" ,r-mixtools) |
| 3070 | ("r-rarpack" ,r-rarpack) |
| 3071 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 3072 | ("r-rhdf5" ,r-rhdf5) |
| 3073 | ("r-ruvseq" ,r-ruvseq) |
| 3074 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 3075 | (home-page "https://bioconductor.org/packages/scone") |
| 3076 | (synopsis "Single cell overview of normalized expression data") |
| 3077 | (description |
| 3078 | "SCONE is an R package for comparing and ranking the performance of |
| 3079 | different normalization schemes for single-cell RNA-seq and other |
| 3080 | high-throughput analyses.") |
| 3081 | (license license:artistic2.0))) |
| 3082 | |
| 3083 | (define-public r-geoquery |
| 3084 | (package |
| 3085 | (name "r-geoquery") |
| 3086 | (version "2.54.1") |
| 3087 | (source |
| 3088 | (origin |
| 3089 | (method url-fetch) |
| 3090 | (uri (bioconductor-uri "GEOquery" version)) |
| 3091 | (sha256 |
| 3092 | (base32 |
| 3093 | "0j8mlldy7dc38fx5zwj6z6l4b9bhvrn8sil3z8asnd4ic7w9ifx5")))) |
| 3094 | (properties `((upstream-name . "GEOquery"))) |
| 3095 | (build-system r-build-system) |
| 3096 | (propagated-inputs |
| 3097 | `(("r-biobase" ,r-biobase) |
| 3098 | ("r-dplyr" ,r-dplyr) |
| 3099 | ("r-httr" ,r-httr) |
| 3100 | ("r-limma" ,r-limma) |
| 3101 | ("r-magrittr" ,r-magrittr) |
| 3102 | ("r-readr" ,r-readr) |
| 3103 | ("r-tidyr" ,r-tidyr) |
| 3104 | ("r-xml2" ,r-xml2))) |
| 3105 | (home-page "https://github.com/seandavi/GEOquery/") |
| 3106 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") |
| 3107 | (description |
| 3108 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of |
| 3109 | microarray data. Given the rich and varied nature of this resource, it is |
| 3110 | only natural to want to apply BioConductor tools to these data. GEOquery is |
| 3111 | the bridge between GEO and BioConductor.") |
| 3112 | (license license:gpl2))) |
| 3113 | |
| 3114 | (define-public r-illuminaio |
| 3115 | (package |
| 3116 | (name "r-illuminaio") |
| 3117 | (version "0.28.0") |
| 3118 | (source |
| 3119 | (origin |
| 3120 | (method url-fetch) |
| 3121 | (uri (bioconductor-uri "illuminaio" version)) |
| 3122 | (sha256 |
| 3123 | (base32 |
| 3124 | "1psza8jq6h8fv2rm91ah67dgjlnj1l80yracwgdl1agd0ycv90sh")))) |
| 3125 | (build-system r-build-system) |
| 3126 | (propagated-inputs |
| 3127 | `(("r-base64" ,r-base64))) |
| 3128 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") |
| 3129 | (synopsis "Parse Illumina microarray output files") |
| 3130 | (description |
| 3131 | "This package provides tools for parsing Illumina's microarray output |
| 3132 | files, including IDAT.") |
| 3133 | (license license:gpl2))) |
| 3134 | |
| 3135 | (define-public r-siggenes |
| 3136 | (package |
| 3137 | (name "r-siggenes") |
| 3138 | (version "1.60.0") |
| 3139 | (source |
| 3140 | (origin |
| 3141 | (method url-fetch) |
| 3142 | (uri (bioconductor-uri "siggenes" version)) |
| 3143 | (sha256 |
| 3144 | (base32 |
| 3145 | "03lmq3hqprwps4miynl2vhqi3v4als5vqmz4lb19lk5a4zja72b4")))) |
| 3146 | (build-system r-build-system) |
| 3147 | (propagated-inputs |
| 3148 | `(("r-biobase" ,r-biobase) |
| 3149 | ("r-multtest" ,r-multtest) |
| 3150 | ("r-scrime" ,r-scrime))) |
| 3151 | (home-page "https://bioconductor.org/packages/siggenes/") |
| 3152 | (synopsis |
| 3153 | "Multiple testing using SAM and Efron's empirical Bayes approaches") |
| 3154 | (description |
| 3155 | "This package provides tools for the identification of differentially |
| 3156 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using |
| 3157 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical |
| 3158 | Bayes Analyses of Microarrays} (EBAM).") |
| 3159 | (license license:lgpl2.0+))) |
| 3160 | |
| 3161 | (define-public r-bumphunter |
| 3162 | (package |
| 3163 | (name "r-bumphunter") |
| 3164 | (version "1.28.0") |
| 3165 | (source |
| 3166 | (origin |
| 3167 | (method url-fetch) |
| 3168 | (uri (bioconductor-uri "bumphunter" version)) |
| 3169 | (sha256 |
| 3170 | (base32 |
| 3171 | "1p3gwb954zns61d1pwgkplxnvgk2lixrl93kkkf439wa3vlgsnjv")))) |
| 3172 | (build-system r-build-system) |
| 3173 | (propagated-inputs |
| 3174 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3175 | ("r-biocgenerics" ,r-biocgenerics) |
| 3176 | ("r-dorng" ,r-dorng) |
| 3177 | ("r-foreach" ,r-foreach) |
| 3178 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3179 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 3180 | ("r-genomicranges" ,r-genomicranges) |
| 3181 | ("r-iranges" ,r-iranges) |
| 3182 | ("r-iterators" ,r-iterators) |
| 3183 | ("r-limma" ,r-limma) |
| 3184 | ("r-locfit" ,r-locfit) |
| 3185 | ("r-matrixstats" ,r-matrixstats) |
| 3186 | ("r-s4vectors" ,r-s4vectors))) |
| 3187 | (home-page "https://github.com/ririzarr/bumphunter") |
| 3188 | (synopsis "Find bumps in genomic data") |
| 3189 | (description |
| 3190 | "This package provides tools for finding bumps in genomic data in order |
| 3191 | to identify differentially methylated regions in epigenetic epidemiology |
| 3192 | studies.") |
| 3193 | (license license:artistic2.0))) |
| 3194 | |
| 3195 | (define-public r-minfi |
| 3196 | (package |
| 3197 | (name "r-minfi") |
| 3198 | (version "1.32.0") |
| 3199 | (source |
| 3200 | (origin |
| 3201 | (method url-fetch) |
| 3202 | (uri (bioconductor-uri "minfi" version)) |
| 3203 | (sha256 |
| 3204 | (base32 |
| 3205 | "177isdvcq2476xybvfbh7x11qsj5nzckgh3b6p156wlx9ap9dvl3")))) |
| 3206 | (build-system r-build-system) |
| 3207 | (propagated-inputs |
| 3208 | `(("r-beanplot" ,r-beanplot) |
| 3209 | ("r-biobase" ,r-biobase) |
| 3210 | ("r-biocgenerics" ,r-biocgenerics) |
| 3211 | ("r-biocparallel" ,r-biocparallel) |
| 3212 | ("r-biostrings" ,r-biostrings) |
| 3213 | ("r-bumphunter" ,r-bumphunter) |
| 3214 | ("r-data-table" ,r-data-table) |
| 3215 | ("r-delayedarray" ,r-delayedarray) |
| 3216 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) |
| 3217 | ("r-genefilter" ,r-genefilter) |
| 3218 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3219 | ("r-genomicranges" ,r-genomicranges) |
| 3220 | ("r-geoquery" ,r-geoquery) |
| 3221 | ("r-hdf5array" ,r-hdf5array) |
| 3222 | ("r-illuminaio" ,r-illuminaio) |
| 3223 | ("r-iranges" ,r-iranges) |
| 3224 | ("r-lattice" ,r-lattice) |
| 3225 | ("r-limma" ,r-limma) |
| 3226 | ("r-mass" ,r-mass) |
| 3227 | ("r-mclust" ,r-mclust) |
| 3228 | ("r-nlme" ,r-nlme) |
| 3229 | ("r-nor1mix" ,r-nor1mix) |
| 3230 | ("r-preprocesscore" ,r-preprocesscore) |
| 3231 | ("r-quadprog" ,r-quadprog) |
| 3232 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 3233 | ("r-reshape" ,r-reshape) |
| 3234 | ("r-s4vectors" ,r-s4vectors) |
| 3235 | ("r-siggenes" ,r-siggenes) |
| 3236 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 3237 | (home-page "https://github.com/hansenlab/minfi") |
| 3238 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") |
| 3239 | (description |
| 3240 | "This package provides tools to analyze and visualize Illumina Infinium |
| 3241 | methylation arrays.") |
| 3242 | (license license:artistic2.0))) |
| 3243 | |
| 3244 | (define-public r-methylumi |
| 3245 | (package |
| 3246 | (name "r-methylumi") |
| 3247 | (version "2.32.0") |
| 3248 | (source |
| 3249 | (origin |
| 3250 | (method url-fetch) |
| 3251 | (uri (bioconductor-uri "methylumi" version)) |
| 3252 | (sha256 |
| 3253 | (base32 |
| 3254 | "0zd4h6n37v3z0mas69z2xsf5s0naih828987m8v0g9hhq4f6hf5w")))) |
| 3255 | (build-system r-build-system) |
| 3256 | (propagated-inputs |
| 3257 | `(("r-annotate" ,r-annotate) |
| 3258 | ("r-annotationdbi" ,r-annotationdbi) |
| 3259 | ("r-biobase" ,r-biobase) |
| 3260 | ("r-biocgenerics" ,r-biocgenerics) |
| 3261 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) |
| 3262 | ("r-genefilter" ,r-genefilter) |
| 3263 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3264 | ("r-genomicranges" ,r-genomicranges) |
| 3265 | ("r-ggplot2" ,r-ggplot2) |
| 3266 | ("r-illuminaio" ,r-illuminaio) |
| 3267 | ("r-iranges" ,r-iranges) |
| 3268 | ("r-lattice" ,r-lattice) |
| 3269 | ("r-matrixstats" ,r-matrixstats) |
| 3270 | ("r-minfi" ,r-minfi) |
| 3271 | ("r-reshape2" ,r-reshape2) |
| 3272 | ("r-s4vectors" ,r-s4vectors) |
| 3273 | ("r-scales" ,r-scales) |
| 3274 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 3275 | (home-page "https://bioconductor.org/packages/methylumi") |
| 3276 | (synopsis "Handle Illumina methylation data") |
| 3277 | (description |
| 3278 | "This package provides classes for holding and manipulating Illumina |
| 3279 | methylation data. Based on eSet, it can contain MIAME information, sample |
| 3280 | information, feature information, and multiple matrices of data. An |
| 3281 | \"intelligent\" import function, methylumiR can read the Illumina text files |
| 3282 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from |
| 3283 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, |
| 3284 | background correction, and quality control features for GoldenGate, Infinium, |
| 3285 | and Infinium HD arrays are also included.") |
| 3286 | (license license:gpl2))) |
| 3287 | |
| 3288 | (define-public r-lumi |
| 3289 | (package |
| 3290 | (name "r-lumi") |
| 3291 | (version "2.38.0") |
| 3292 | (source |
| 3293 | (origin |
| 3294 | (method url-fetch) |
| 3295 | (uri (bioconductor-uri "lumi" version)) |
| 3296 | (sha256 |
| 3297 | (base32 |
| 3298 | "0lgrqbdvp7ykcafc0bpnbcsf396na3jj5c35x9ysf5bpcas23nmm")))) |
| 3299 | (build-system r-build-system) |
| 3300 | (propagated-inputs |
| 3301 | `(("r-affy" ,r-affy) |
| 3302 | ("r-annotate" ,r-annotate) |
| 3303 | ("r-annotationdbi" ,r-annotationdbi) |
| 3304 | ("r-biobase" ,r-biobase) |
| 3305 | ("r-dbi" ,r-dbi) |
| 3306 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 3307 | ("r-genomicranges" ,r-genomicranges) |
| 3308 | ("r-kernsmooth" ,r-kernsmooth) |
| 3309 | ("r-lattice" ,r-lattice) |
| 3310 | ("r-mass" ,r-mass) |
| 3311 | ("r-methylumi" ,r-methylumi) |
| 3312 | ("r-mgcv" ,r-mgcv) |
| 3313 | ("r-nleqslv" ,r-nleqslv) |
| 3314 | ("r-preprocesscore" ,r-preprocesscore) |
| 3315 | ("r-rsqlite" ,r-rsqlite))) |
| 3316 | (home-page "https://bioconductor.org/packages/lumi") |
| 3317 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") |
| 3318 | (description |
| 3319 | "The lumi package provides an integrated solution for the Illumina |
| 3320 | microarray data analysis. It includes functions of Illumina |
| 3321 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific |
| 3322 | variance stabilization, normalization and gene annotation at the probe level. |
| 3323 | It also includes the functions of processing Illumina methylation microarrays, |
| 3324 | especially Illumina Infinium methylation microarrays.") |
| 3325 | (license license:lgpl2.0+))) |
| 3326 | |
| 3327 | (define-public r-linnorm |
| 3328 | (package |
| 3329 | (name "r-linnorm") |
| 3330 | (version "2.10.0") |
| 3331 | (source |
| 3332 | (origin |
| 3333 | (method url-fetch) |
| 3334 | (uri (bioconductor-uri "Linnorm" version)) |
| 3335 | (sha256 |
| 3336 | (base32 |
| 3337 | "15mhwiqmp9m65zvrdbr2hhy3x81lf4jbwgjsf75g41if2v2g8x67")))) |
| 3338 | (properties `((upstream-name . "Linnorm"))) |
| 3339 | (build-system r-build-system) |
| 3340 | (propagated-inputs |
| 3341 | `(("r-amap" ,r-amap) |
| 3342 | ("r-apcluster" ,r-apcluster) |
| 3343 | ("r-ellipse" ,r-ellipse) |
| 3344 | ("r-fastcluster" ,r-fastcluster) |
| 3345 | ("r-fpc" ,r-fpc) |
| 3346 | ("r-ggdendro" ,r-ggdendro) |
| 3347 | ("r-ggplot2" ,r-ggplot2) |
| 3348 | ("r-gmodels" ,r-gmodels) |
| 3349 | ("r-igraph" ,r-igraph) |
| 3350 | ("r-limma" ,r-limma) |
| 3351 | ("r-mass" ,r-mass) |
| 3352 | ("r-mclust" ,r-mclust) |
| 3353 | ("r-rcpp" ,r-rcpp) |
| 3354 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
| 3355 | ("r-rtsne" ,r-rtsne) |
| 3356 | ("r-statmod" ,r-statmod) |
| 3357 | ("r-vegan" ,r-vegan) |
| 3358 | ("r-zoo" ,r-zoo))) |
| 3359 | (home-page "http://www.jjwanglab.org/Linnorm/") |
| 3360 | (synopsis "Linear model and normality based transformation method") |
| 3361 | (description |
| 3362 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq |
| 3363 | count data or any large scale count data. It transforms such datasets for |
| 3364 | parametric tests. In addition to the transformtion function (@code{Linnorm}), |
| 3365 | the following pipelines are implemented: |
| 3366 | |
| 3367 | @enumerate |
| 3368 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) |
| 3369 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means |
| 3370 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, |
| 3371 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) |
| 3372 | @item Differential expression analysis or differential peak detection using |
| 3373 | limma (@code{Linnorm.limma}) |
| 3374 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) |
| 3375 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) |
| 3376 | @item Stable gene selection for scRNA-seq data; for users without or who do |
| 3377 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) |
| 3378 | @item Data imputation (@code{Linnorm.DataImput}). |
| 3379 | @end enumerate |
| 3380 | |
| 3381 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the |
| 3382 | @code{RnaXSim} function is included for simulating RNA-seq data for the |
| 3383 | evaluation of DEG analysis methods.") |
| 3384 | (license license:expat))) |
| 3385 | |
| 3386 | (define-public r-ioniser |
| 3387 | (package |
| 3388 | (name "r-ioniser") |
| 3389 | (version "2.10.0") |
| 3390 | (source |
| 3391 | (origin |
| 3392 | (method url-fetch) |
| 3393 | (uri (bioconductor-uri "IONiseR" version)) |
| 3394 | (sha256 |
| 3395 | (base32 |
| 3396 | "1c265bzh923i9mw83mjpj0bzbkixbs6sg1h1z51y9xjkakdgg90f")))) |
| 3397 | (properties `((upstream-name . "IONiseR"))) |
| 3398 | (build-system r-build-system) |
| 3399 | (propagated-inputs |
| 3400 | `(("r-biocgenerics" ,r-biocgenerics) |
| 3401 | ("r-biocparallel" ,r-biocparallel) |
| 3402 | ("r-biostrings" ,r-biostrings) |
| 3403 | ("r-bit64" ,r-bit64) |
| 3404 | ("r-dplyr" ,r-dplyr) |
| 3405 | ("r-ggplot2" ,r-ggplot2) |
| 3406 | ("r-magrittr" ,r-magrittr) |
| 3407 | ("r-rhdf5" ,r-rhdf5) |
| 3408 | ("r-shortread" ,r-shortread) |
| 3409 | ("r-stringr" ,r-stringr) |
| 3410 | ("r-tibble" ,r-tibble) |
| 3411 | ("r-tidyr" ,r-tidyr) |
| 3412 | ("r-xvector" ,r-xvector))) |
| 3413 | (home-page "https://bioconductor.org/packages/IONiseR/") |
| 3414 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") |
| 3415 | (description |
| 3416 | "IONiseR provides tools for the quality assessment of Oxford Nanopore |
| 3417 | MinION data. It extracts summary statistics from a set of fast5 files and can |
| 3418 | be used either before or after base calling. In addition to standard |
| 3419 | summaries of the read-types produced, it provides a number of plots for |
| 3420 | visualising metrics relative to experiment run time or spatially over the |
| 3421 | surface of a flowcell.") |
| 3422 | (license license:expat))) |
| 3423 | |
| 3424 | ;; This is a CRAN package, but it depends on packages from Bioconductor. |
| 3425 | (define-public r-gkmsvm |
| 3426 | (package |
| 3427 | (name "r-gkmsvm") |
| 3428 | (version "0.80.0") |
| 3429 | (source |
| 3430 | (origin |
| 3431 | (method url-fetch) |
| 3432 | (uri (cran-uri "gkmSVM" version)) |
| 3433 | (sha256 |
| 3434 | (base32 |
| 3435 | "0ljcga246ad0ql8x3drvrdsyp0f20mgp3p6lnl79xb76qgfdnm0p")))) |
| 3436 | (properties `((upstream-name . "gkmSVM"))) |
| 3437 | (build-system r-build-system) |
| 3438 | (propagated-inputs |
| 3439 | `(("r-kernlab" ,r-kernlab) |
| 3440 | ("r-rcpp" ,r-rcpp) |
| 3441 | ("r-rocr" ,r-rocr) |
| 3442 | ("r-seqinr" ,r-seqinr))) |
| 3443 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") |
| 3444 | (synopsis "Gapped-kmer support vector machine") |
| 3445 | (description |
| 3446 | "This R package provides tools for training gapped-kmer SVM classifiers |
| 3447 | for DNA and protein sequences. This package supports several sequence |
| 3448 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") |
| 3449 | (license license:gpl2+))) |
| 3450 | |
| 3451 | ;; This is a CRAN package, but it depends on multtest from Bioconductor. |
| 3452 | (define-public r-mutoss |
| 3453 | (package |
| 3454 | (name "r-mutoss") |
| 3455 | (version "0.1-12") |
| 3456 | (source |
| 3457 | (origin |
| 3458 | (method url-fetch) |
| 3459 | (uri (cran-uri "mutoss" version)) |
| 3460 | (sha256 |
| 3461 | (base32 |
| 3462 | "1yk7p7pb2xm38d3j19ysgwmix48lvimbhkhjjwk5jmr1a0ysx298")))) |
| 3463 | (properties `((upstream-name . "mutoss"))) |
| 3464 | (build-system r-build-system) |
| 3465 | (propagated-inputs |
| 3466 | `(("r-multcomp" ,r-multcomp) |
| 3467 | ("r-multtest" ,r-multtest) |
| 3468 | ("r-mvtnorm" ,r-mvtnorm) |
| 3469 | ("r-plotrix" ,r-plotrix))) |
| 3470 | (home-page "https://github.com/kornl/mutoss/") |
| 3471 | (synopsis "Unified multiple testing procedures") |
| 3472 | (description |
| 3473 | "This package is designed to ease the application and comparison of |
| 3474 | multiple hypothesis testing procedures for FWER, gFWER, FDR and FDX. Methods |
| 3475 | are standardized and usable by the accompanying mutossGUI package.") |
| 3476 | ;; Any version of the GPL. |
| 3477 | (license (list license:gpl2+ license:gpl3+)))) |
| 3478 | |
| 3479 | ;; This is a CRAN package, but it depends on mutoss, which depends on multtest |
| 3480 | ;; from Bioconductor, so we put it here. |
| 3481 | (define-public r-metap |
| 3482 | (package |
| 3483 | (name "r-metap") |
| 3484 | (version "1.3") |
| 3485 | (source |
| 3486 | (origin |
| 3487 | (method url-fetch) |
| 3488 | (uri (cran-uri "metap" version)) |
| 3489 | (sha256 |
| 3490 | (base32 |
| 3491 | "1jmmmmjiklaxfl604hwqil193ydaghvd5jv8xsr4bx3pzn5i9kvz")))) |
| 3492 | (build-system r-build-system) |
| 3493 | (propagated-inputs |
| 3494 | `(("r-lattice" ,r-lattice) |
| 3495 | ("r-mutoss" ,r-mutoss) |
| 3496 | ("r-rdpack" ,r-rdpack) |
| 3497 | ("r-tfisher" ,r-tfisher))) |
| 3498 | (home-page "http://www.dewey.myzen.co.uk/meta/meta.html") |
| 3499 | (synopsis "Meta-analysis of significance values") |
| 3500 | (description |
| 3501 | "The canonical way to perform meta-analysis involves using effect sizes. |
| 3502 | When they are not available this package provides a number of methods for |
| 3503 | meta-analysis of significance values including the methods of Edgington, |
| 3504 | Fisher, Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate |
| 3505 | published results; and a routine for graphical display.") |
| 3506 | (license license:gpl2))) |
| 3507 | |
| 3508 | (define-public r-triform |
| 3509 | (package |
| 3510 | (name "r-triform") |
| 3511 | (version "1.28.0") |
| 3512 | (source |
| 3513 | (origin |
| 3514 | (method url-fetch) |
| 3515 | (uri (bioconductor-uri "triform" version)) |
| 3516 | (sha256 |
| 3517 | (base32 |
| 3518 | "12qdyrcw2mcawqdw65v0hjaghzlwa10xl6j8458izcrm5k6dlvz9")))) |
| 3519 | (build-system r-build-system) |
| 3520 | (propagated-inputs |
| 3521 | `(("r-biocgenerics" ,r-biocgenerics) |
| 3522 | ("r-iranges" ,r-iranges) |
| 3523 | ("r-yaml" ,r-yaml))) |
| 3524 | (home-page "https://bioconductor.org/packages/triform/") |
| 3525 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") |
| 3526 | (description |
| 3527 | "The Triform algorithm uses model-free statistics to identify peak-like |
| 3528 | distributions of TF ChIP sequencing reads, taking advantage of an improved |
| 3529 | peak definition in combination with known profile characteristics.") |
| 3530 | (license license:gpl2))) |
| 3531 | |
| 3532 | (define-public r-varianttools |
| 3533 | (package |
| 3534 | (name "r-varianttools") |
| 3535 | (version "1.28.1") |
| 3536 | (source |
| 3537 | (origin |
| 3538 | (method url-fetch) |
| 3539 | (uri (bioconductor-uri "VariantTools" version)) |
| 3540 | (sha256 |
| 3541 | (base32 |
| 3542 | "1x57shc3slcbnc807ra1nwnjr37sqjh04n2xfwd469m4hkjb0jzh")))) |
| 3543 | (properties `((upstream-name . "VariantTools"))) |
| 3544 | (build-system r-build-system) |
| 3545 | (propagated-inputs |
| 3546 | `(("r-biobase" ,r-biobase) |
| 3547 | ("r-biocgenerics" ,r-biocgenerics) |
| 3548 | ("r-biocparallel" ,r-biocparallel) |
| 3549 | ("r-biostrings" ,r-biostrings) |
| 3550 | ("r-bsgenome" ,r-bsgenome) |
| 3551 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3552 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 3553 | ("r-genomicranges" ,r-genomicranges) |
| 3554 | ("r-iranges" ,r-iranges) |
| 3555 | ("r-matrix" ,r-matrix) |
| 3556 | ("r-rsamtools" ,r-rsamtools) |
| 3557 | ("r-rtracklayer" ,r-rtracklayer) |
| 3558 | ("r-s4vectors" ,r-s4vectors) |
| 3559 | ("r-variantannotation" ,r-variantannotation))) |
| 3560 | (home-page "https://bioconductor.org/packages/VariantTools/") |
| 3561 | (synopsis "Tools for exploratory analysis of variant calls") |
| 3562 | (description |
| 3563 | "Explore, diagnose, and compare variant calls using filters. The |
| 3564 | VariantTools package supports a workflow for loading data, calling single |
| 3565 | sample variants and tumor-specific somatic mutations or other sample-specific |
| 3566 | variant types (e.g., RNA editing). Most of the functions operate on |
| 3567 | alignments (BAM files) or datasets of called variants. The user is expected |
| 3568 | to have already aligned the reads with a separate tool, e.g., GSNAP via |
| 3569 | gmapR.") |
| 3570 | (license license:artistic2.0))) |
| 3571 | |
| 3572 | (define-public r-heatplus |
| 3573 | (package |
| 3574 | (name "r-heatplus") |
| 3575 | (version "2.32.1") |
| 3576 | (source |
| 3577 | (origin |
| 3578 | (method url-fetch) |
| 3579 | (uri (bioconductor-uri "Heatplus" version)) |
| 3580 | (sha256 |
| 3581 | (base32 |
| 3582 | "1ldxj2hasg6ysh70sc73mz2v4h3n8gf3lii09c3sqc4wmz5h7rp1")))) |
| 3583 | (properties `((upstream-name . "Heatplus"))) |
| 3584 | (build-system r-build-system) |
| 3585 | (propagated-inputs |
| 3586 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 3587 | (home-page "https://github.com/alexploner/Heatplus") |
| 3588 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") |
| 3589 | (description |
| 3590 | "This package provides tools to display a rectangular heatmap (intensity |
| 3591 | plot) of a data matrix. By default, both samples (columns) and features (row) |
| 3592 | of the matrix are sorted according to a hierarchical clustering, and the |
| 3593 | corresponding dendrogram is plotted. Optionally, panels with additional |
| 3594 | information about samples and features can be added to the plot.") |
| 3595 | (license license:gpl2+))) |
| 3596 | |
| 3597 | (define-public r-gosemsim |
| 3598 | (package |
| 3599 | (name "r-gosemsim") |
| 3600 | (version "2.12.1") |
| 3601 | (source |
| 3602 | (origin |
| 3603 | (method url-fetch) |
| 3604 | (uri (bioconductor-uri "GOSemSim" version)) |
| 3605 | (sha256 |
| 3606 | (base32 |
| 3607 | "1r8yx6qw6d6602cp8aspzl3shi1l1zqcrc8fm9d5wg01sw1whs05")))) |
| 3608 | (properties `((upstream-name . "GOSemSim"))) |
| 3609 | (build-system r-build-system) |
| 3610 | (propagated-inputs |
| 3611 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3612 | ("r-go-db" ,r-go-db) |
| 3613 | ("r-rcpp" ,r-rcpp))) |
| 3614 | (native-inputs |
| 3615 | `(("r-knitr" ,r-knitr))) |
| 3616 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") |
| 3617 | (synopsis "GO-terms semantic similarity measures") |
| 3618 | (description |
| 3619 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide |
| 3620 | quantitative ways to compute similarities between genes and gene groups, and |
| 3621 | have became important basis for many bioinformatics analysis approaches. |
| 3622 | GOSemSim is an R package for semantic similarity computation among GO terms, |
| 3623 | sets of GO terms, gene products and gene clusters.") |
| 3624 | (license license:artistic2.0))) |
| 3625 | |
| 3626 | (define-public r-anota |
| 3627 | (package |
| 3628 | (name "r-anota") |
| 3629 | (version "1.34.0") |
| 3630 | (source |
| 3631 | (origin |
| 3632 | (method url-fetch) |
| 3633 | (uri (bioconductor-uri "anota" version)) |
| 3634 | (sha256 |
| 3635 | (base32 |
| 3636 | "1bkavzrxy1bjz0bwapwa9i3ysln7gljgziwd8c05fmg2f46j1z6m")))) |
| 3637 | (build-system r-build-system) |
| 3638 | (propagated-inputs |
| 3639 | `(("r-multtest" ,r-multtest) |
| 3640 | ("r-qvalue" ,r-qvalue))) |
| 3641 | (home-page "https://bioconductor.org/packages/anota/") |
| 3642 | (synopsis "Analysis of translational activity") |
| 3643 | (description |
| 3644 | "Genome wide studies of translational control is emerging as a tool to |
| 3645 | study various biological conditions. The output from such analysis is both |
| 3646 | the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively |
| 3647 | involved in translation (the actively translating mRNA level) for each mRNA. |
| 3648 | The standard analysis of such data strives towards identifying differential |
| 3649 | translational between two or more sample classes - i.e. differences in |
| 3650 | actively translated mRNA levels that are independent of underlying differences |
| 3651 | in cytosolic mRNA levels. This package allows for such analysis using partial |
| 3652 | variances and the random variance model. As 10s of thousands of mRNAs are |
| 3653 | analyzed in parallel the library performs a number of tests to assure that |
| 3654 | the data set is suitable for such analysis.") |
| 3655 | (license license:gpl3))) |
| 3656 | |
| 3657 | (define-public r-sigpathway |
| 3658 | (package |
| 3659 | (name "r-sigpathway") |
| 3660 | (version "1.54.0") |
| 3661 | (source |
| 3662 | (origin |
| 3663 | (method url-fetch) |
| 3664 | (uri (bioconductor-uri "sigPathway" version)) |
| 3665 | (sha256 |
| 3666 | (base32 |
| 3667 | "057qdkbfldpy6hsysk9mrs1vvsqgyl9yx2s6c2f26jz1pardkbqb")))) |
| 3668 | (properties `((upstream-name . "sigPathway"))) |
| 3669 | (build-system r-build-system) |
| 3670 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") |
| 3671 | (synopsis "Pathway analysis") |
| 3672 | (description |
| 3673 | "This package is used to conduct pathway analysis by calculating the NT_k |
| 3674 | and NE_k statistics in a statistical framework for determining whether a |
| 3675 | specified group of genes for a pathway has a coordinated association with a |
| 3676 | phenotype of interest.") |
| 3677 | (license license:gpl2))) |
| 3678 | |
| 3679 | (define-public r-fgsea |
| 3680 | (package |
| 3681 | (name "r-fgsea") |
| 3682 | (version "1.12.0") |
| 3683 | (source |
| 3684 | (origin |
| 3685 | (method url-fetch) |
| 3686 | (uri (bioconductor-uri "fgsea" version)) |
| 3687 | (sha256 |
| 3688 | (base32 |
| 3689 | "0pbq3g515kcbi4wvfx8m09p01h2f8vwsi1qqsyahxz4r1fasz4c1")))) |
| 3690 | (build-system r-build-system) |
| 3691 | (propagated-inputs |
| 3692 | `(("r-bh" ,r-bh) |
| 3693 | ("r-biocparallel" ,r-biocparallel) |
| 3694 | ("r-data-table" ,r-data-table) |
| 3695 | ("r-fastmatch" ,r-fastmatch) |
| 3696 | ("r-ggplot2" ,r-ggplot2) |
| 3697 | ("r-gridextra" ,r-gridextra) |
| 3698 | ("r-matrix" ,r-matrix) |
| 3699 | ("r-rcpp" ,r-rcpp))) |
| 3700 | (home-page "https://github.com/ctlab/fgsea/") |
| 3701 | (synopsis "Fast gene set enrichment analysis") |
| 3702 | (description |
| 3703 | "The package implements an algorithm for fast gene set enrichment |
| 3704 | analysis. Using the fast algorithm makes more permutations and gets |
| 3705 | more fine grained p-values, which allows using accurate standard approaches |
| 3706 | to multiple hypothesis correction.") |
| 3707 | (license license:expat))) |
| 3708 | |
| 3709 | (define-public r-dose |
| 3710 | (package |
| 3711 | (name "r-dose") |
| 3712 | (version "3.12.0") |
| 3713 | (source |
| 3714 | (origin |
| 3715 | (method url-fetch) |
| 3716 | (uri (bioconductor-uri "DOSE" version)) |
| 3717 | (sha256 |
| 3718 | (base32 |
| 3719 | "0ss8mr28q0vswxjmhcas0aqag5nl099jbyn5w3ypbbxqwfvf9jj5")))) |
| 3720 | (properties `((upstream-name . "DOSE"))) |
| 3721 | (build-system r-build-system) |
| 3722 | (propagated-inputs |
| 3723 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3724 | ("r-biocparallel" ,r-biocparallel) |
| 3725 | ("r-do-db" ,r-do-db) |
| 3726 | ("r-fgsea" ,r-fgsea) |
| 3727 | ("r-ggplot2" ,r-ggplot2) |
| 3728 | ("r-gosemsim" ,r-gosemsim) |
| 3729 | ("r-qvalue" ,r-qvalue) |
| 3730 | ("r-reshape2" ,r-reshape2) |
| 3731 | ("r-s4vectors" ,r-s4vectors))) |
| 3732 | (native-inputs |
| 3733 | `(("r-knitr" ,r-knitr))) |
| 3734 | (home-page "https://guangchuangyu.github.io/software/DOSE/") |
| 3735 | (synopsis "Disease ontology semantic and enrichment analysis") |
| 3736 | (description |
| 3737 | "This package implements five methods proposed by Resnik, Schlicker, |
| 3738 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among |
| 3739 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses |
| 3740 | including hypergeometric model and gene set enrichment analysis are also |
| 3741 | implemented for discovering disease associations of high-throughput biological |
| 3742 | data.") |
| 3743 | (license license:artistic2.0))) |
| 3744 | |
| 3745 | (define-public r-enrichplot |
| 3746 | (package |
| 3747 | (name "r-enrichplot") |
| 3748 | (version "1.6.1") |
| 3749 | (source |
| 3750 | (origin |
| 3751 | (method url-fetch) |
| 3752 | (uri (bioconductor-uri "enrichplot" version)) |
| 3753 | (sha256 |
| 3754 | (base32 |
| 3755 | "0707f5ll58psh7pr001cmmk5di7dprnbry1cy2mw20vn8p24nf3x")))) |
| 3756 | (build-system r-build-system) |
| 3757 | (propagated-inputs |
| 3758 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3759 | ("r-cowplot" ,r-cowplot) |
| 3760 | ("r-dose" ,r-dose) |
| 3761 | ("r-europepmc" ,r-europepmc) |
| 3762 | ("r-ggplot2" ,r-ggplot2) |
| 3763 | ("r-ggplotify" ,r-ggplotify) |
| 3764 | ("r-ggraph" ,r-ggraph) |
| 3765 | ("r-ggridges" ,r-ggridges) |
| 3766 | ("r-gosemsim" ,r-gosemsim) |
| 3767 | ("r-gridextra" ,r-gridextra) |
| 3768 | ("r-igraph" ,r-igraph) |
| 3769 | ("r-purrr" ,r-purrr) |
| 3770 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 3771 | ("r-reshape2" ,r-reshape2))) |
| 3772 | (home-page "https://github.com/GuangchuangYu/enrichplot") |
| 3773 | (synopsis "Visualization of functional enrichment result") |
| 3774 | (description |
| 3775 | "The enrichplot package implements several visualization methods for |
| 3776 | interpreting functional enrichment results obtained from ORA or GSEA analyses. |
| 3777 | All the visualization methods are developed based on ggplot2 graphics.") |
| 3778 | (license license:artistic2.0))) |
| 3779 | |
| 3780 | (define-public r-clusterprofiler |
| 3781 | (package |
| 3782 | (name "r-clusterprofiler") |
| 3783 | (version "3.14.3") |
| 3784 | (source |
| 3785 | (origin |
| 3786 | (method url-fetch) |
| 3787 | (uri (bioconductor-uri "clusterProfiler" version)) |
| 3788 | (sha256 |
| 3789 | (base32 |
| 3790 | "08pd7bmqmyxncj09ilz8yb9sf1pv9ni98y8b93pz2giy7pl407hg")))) |
| 3791 | (properties |
| 3792 | `((upstream-name . "clusterProfiler"))) |
| 3793 | (build-system r-build-system) |
| 3794 | (propagated-inputs |
| 3795 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3796 | ("r-dose" ,r-dose) |
| 3797 | ("r-enrichplot" ,r-enrichplot) |
| 3798 | ("r-ggplot2" ,r-ggplot2) |
| 3799 | ("r-go-db" ,r-go-db) |
| 3800 | ("r-gosemsim" ,r-gosemsim) |
| 3801 | ("r-magrittr" ,r-magrittr) |
| 3802 | ("r-plyr" ,r-plyr) |
| 3803 | ("r-qvalue" ,r-qvalue) |
| 3804 | ("r-rvcheck" ,r-rvcheck) |
| 3805 | ("r-tidyr" ,r-tidyr))) |
| 3806 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") |
| 3807 | (synopsis "Analysis and visualization of functional profiles for gene clusters") |
| 3808 | (description |
| 3809 | "This package implements methods to analyze and visualize functional |
| 3810 | profiles (GO and KEGG) of gene and gene clusters.") |
| 3811 | (license license:artistic2.0))) |
| 3812 | |
| 3813 | (define-public r-mlinterfaces |
| 3814 | (package |
| 3815 | (name "r-mlinterfaces") |
| 3816 | (version "1.66.5") |
| 3817 | (source |
| 3818 | (origin |
| 3819 | (method url-fetch) |
| 3820 | (uri (bioconductor-uri "MLInterfaces" version)) |
| 3821 | (sha256 |
| 3822 | (base32 |
| 3823 | "05bg7qcrv485m03rkyq3qg5hrr1m3y7zx49bipwaivzqm3s1mbw5")))) |
| 3824 | (properties `((upstream-name . "MLInterfaces"))) |
| 3825 | (build-system r-build-system) |
| 3826 | (propagated-inputs |
| 3827 | `(("r-annotate" ,r-annotate) |
| 3828 | ("r-biobase" ,r-biobase) |
| 3829 | ("r-biocgenerics" ,r-biocgenerics) |
| 3830 | ("r-cluster" ,r-cluster) |
| 3831 | ("r-fpc" ,r-fpc) |
| 3832 | ("r-gbm" ,r-gbm) |
| 3833 | ("r-gdata" ,r-gdata) |
| 3834 | ("r-genefilter" ,r-genefilter) |
| 3835 | ("r-ggvis" ,r-ggvis) |
| 3836 | ("r-hwriter" ,r-hwriter) |
| 3837 | ("r-mass" ,r-mass) |
| 3838 | ("r-mlbench" ,r-mlbench) |
| 3839 | ("r-pls" ,r-pls) |
| 3840 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 3841 | ("r-rpart" ,r-rpart) |
| 3842 | ("r-sfsmisc" ,r-sfsmisc) |
| 3843 | ("r-shiny" ,r-shiny) |
| 3844 | ("r-threejs" ,r-threejs))) |
| 3845 | (home-page "https://bioconductor.org/packages/MLInterfaces/") |
| 3846 | (synopsis "Interfaces to R machine learning procedures") |
| 3847 | (description |
| 3848 | "This package provides uniform interfaces to machine learning code for |
| 3849 | data in R and Bioconductor containers.") |
| 3850 | ;; Any version of the LGPL. |
| 3851 | (license license:lgpl2.1+))) |
| 3852 | |
| 3853 | (define-public r-annaffy |
| 3854 | (package |
| 3855 | (name "r-annaffy") |
| 3856 | (version "1.58.0") |
| 3857 | (source |
| 3858 | (origin |
| 3859 | (method url-fetch) |
| 3860 | (uri (bioconductor-uri "annaffy" version)) |
| 3861 | (sha256 |
| 3862 | (base32 |
| 3863 | "1jrf4bq2wky4ay1jrcy60si6hxdcn4j05w5vgs38yfb92gq77i16")))) |
| 3864 | (build-system r-build-system) |
| 3865 | (arguments |
| 3866 | `(#:phases |
| 3867 | (modify-phases %standard-phases |
| 3868 | (add-after 'unpack 'remove-reference-to-non-free-data |
| 3869 | (lambda _ |
| 3870 | (substitute* "DESCRIPTION" |
| 3871 | ((", KEGG.db") "")) |
| 3872 | #t))))) |
| 3873 | (propagated-inputs |
| 3874 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3875 | ("r-biobase" ,r-biobase) |
| 3876 | ("r-dbi" ,r-dbi) |
| 3877 | ("r-go-db" ,r-go-db))) |
| 3878 | (home-page "https://bioconductor.org/packages/annaffy/") |
| 3879 | (synopsis "Annotation tools for Affymetrix biological metadata") |
| 3880 | (description |
| 3881 | "This package provides functions for handling data from Bioconductor |
| 3882 | Affymetrix annotation data packages. It produces compact HTML and text |
| 3883 | reports including experimental data and URL links to many online databases. |
| 3884 | It allows searching of biological metadata using various criteria.") |
| 3885 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of |
| 3886 | ;; the LGPL 2.1 is included. |
| 3887 | (license license:lgpl2.1+))) |
| 3888 | |
| 3889 | (define-public r-a4core |
| 3890 | (package |
| 3891 | (name "r-a4core") |
| 3892 | (version "1.34.0") |
| 3893 | (source |
| 3894 | (origin |
| 3895 | (method url-fetch) |
| 3896 | (uri (bioconductor-uri "a4Core" version)) |
| 3897 | (sha256 |
| 3898 | (base32 |
| 3899 | "0xcs9wl2yrprl4yc0z5s4zrkil3752k9xc1fi8fcx7zab1mm80df")))) |
| 3900 | (properties `((upstream-name . "a4Core"))) |
| 3901 | (build-system r-build-system) |
| 3902 | (propagated-inputs |
| 3903 | `(("r-biobase" ,r-biobase) |
| 3904 | ("r-glmnet" ,r-glmnet))) |
| 3905 | (home-page "https://bioconductor.org/packages/a4Core") |
| 3906 | (synopsis "Automated Affymetrix array analysis core package") |
| 3907 | (description |
| 3908 | "This is the core package for the automated analysis of Affymetrix |
| 3909 | arrays.") |
| 3910 | (license license:gpl3))) |
| 3911 | |
| 3912 | (define-public r-a4classif |
| 3913 | (package |
| 3914 | (name "r-a4classif") |
| 3915 | (version "1.34.0") |
| 3916 | (source |
| 3917 | (origin |
| 3918 | (method url-fetch) |
| 3919 | (uri (bioconductor-uri "a4Classif" version)) |
| 3920 | (sha256 |
| 3921 | (base32 |
| 3922 | "0gj3hdflfs1ybc2kshl9w1dzy0rfzppfj08hx3wa2chjsm0m9brn")))) |
| 3923 | (properties `((upstream-name . "a4Classif"))) |
| 3924 | (build-system r-build-system) |
| 3925 | (propagated-inputs |
| 3926 | `(("r-a4core" ,r-a4core) |
| 3927 | ("r-a4preproc" ,r-a4preproc) |
| 3928 | ("r-glmnet" ,r-glmnet) |
| 3929 | ("r-mlinterfaces" ,r-mlinterfaces) |
| 3930 | ("r-pamr" ,r-pamr) |
| 3931 | ("r-rocr" ,r-rocr) |
| 3932 | ("r-varselrf" ,r-varselrf))) |
| 3933 | (home-page "https://bioconductor.org/packages/a4Classif/") |
| 3934 | (synopsis "Automated Affymetrix array analysis classification package") |
| 3935 | (description |
| 3936 | "This is the classification package for the automated analysis of |
| 3937 | Affymetrix arrays.") |
| 3938 | (license license:gpl3))) |
| 3939 | |
| 3940 | (define-public r-a4preproc |
| 3941 | (package |
| 3942 | (name "r-a4preproc") |
| 3943 | (version "1.34.0") |
| 3944 | (source |
| 3945 | (origin |
| 3946 | (method url-fetch) |
| 3947 | (uri (bioconductor-uri "a4Preproc" version)) |
| 3948 | (sha256 |
| 3949 | (base32 |
| 3950 | "11j5nc33gd6yis1fyagr0y39g21bzkc59kq8b8sd6b3pfc84zrjd")))) |
| 3951 | (properties `((upstream-name . "a4Preproc"))) |
| 3952 | (build-system r-build-system) |
| 3953 | (propagated-inputs |
| 3954 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 3955 | (home-page "https://bioconductor.org/packages/a4Preproc/") |
| 3956 | (synopsis "Automated Affymetrix array analysis preprocessing package") |
| 3957 | (description |
| 3958 | "This is a package for the automated analysis of Affymetrix arrays. It |
| 3959 | is used for preprocessing the arrays.") |
| 3960 | (license license:gpl3))) |
| 3961 | |
| 3962 | (define-public r-a4reporting |
| 3963 | (package |
| 3964 | (name "r-a4reporting") |
| 3965 | (version "1.34.0") |
| 3966 | (source |
| 3967 | (origin |
| 3968 | (method url-fetch) |
| 3969 | (uri (bioconductor-uri "a4Reporting" version)) |
| 3970 | (sha256 |
| 3971 | (base32 |
| 3972 | "15nd4pa5hkdzkhinvqw5ijdqb7k5gk37v2hmk3jsg2d6m0jqphi5")))) |
| 3973 | (properties `((upstream-name . "a4Reporting"))) |
| 3974 | (build-system r-build-system) |
| 3975 | (propagated-inputs |
| 3976 | `(("r-annaffy" ,r-annaffy) |
| 3977 | ("r-xtable" ,r-xtable))) |
| 3978 | (home-page "https://bioconductor.org/packages/a4Reporting/") |
| 3979 | (synopsis "Automated Affymetrix array analysis reporting package") |
| 3980 | (description |
| 3981 | "This is a package for the automated analysis of Affymetrix arrays. It |
| 3982 | provides reporting features.") |
| 3983 | (license license:gpl3))) |
| 3984 | |
| 3985 | (define-public r-a4base |
| 3986 | (package |
| 3987 | (name "r-a4base") |
| 3988 | (version "1.34.1") |
| 3989 | (source |
| 3990 | (origin |
| 3991 | (method url-fetch) |
| 3992 | (uri (bioconductor-uri "a4Base" version)) |
| 3993 | (sha256 |
| 3994 | (base32 |
| 3995 | "1a0yk05ikk1hr1vpxynydrb5xb1hj4hdqlh9zd13n83ir89dss83")))) |
| 3996 | (properties `((upstream-name . "a4Base"))) |
| 3997 | (build-system r-build-system) |
| 3998 | (propagated-inputs |
| 3999 | `(("r-a4core" ,r-a4core) |
| 4000 | ("r-a4preproc" ,r-a4preproc) |
| 4001 | ("r-annaffy" ,r-annaffy) |
| 4002 | ("r-annotationdbi" ,r-annotationdbi) |
| 4003 | ("r-biobase" ,r-biobase) |
| 4004 | ("r-genefilter" ,r-genefilter) |
| 4005 | ("r-glmnet" ,r-glmnet) |
| 4006 | ("r-gplots" ,r-gplots) |
| 4007 | ("r-limma" ,r-limma) |
| 4008 | ("r-mpm" ,r-mpm) |
| 4009 | ("r-multtest" ,r-multtest))) |
| 4010 | (home-page "https://bioconductor.org/packages/a4Base/") |
| 4011 | (synopsis "Automated Affymetrix array analysis base package") |
| 4012 | (description |
| 4013 | "This package provides basic features for the automated analysis of |
| 4014 | Affymetrix arrays.") |
| 4015 | (license license:gpl3))) |
| 4016 | |
| 4017 | (define-public r-a4 |
| 4018 | (package |
| 4019 | (name "r-a4") |
| 4020 | (version "1.34.0") |
| 4021 | (source |
| 4022 | (origin |
| 4023 | (method url-fetch) |
| 4024 | (uri (bioconductor-uri "a4" version)) |
| 4025 | (sha256 |
| 4026 | (base32 |
| 4027 | "14yipy6s2wqr9q0yp09x1mm17npknrhs6yd34i3wrb5id64ywnq4")))) |
| 4028 | (build-system r-build-system) |
| 4029 | (propagated-inputs |
| 4030 | `(("r-a4base" ,r-a4base) |
| 4031 | ("r-a4classif" ,r-a4classif) |
| 4032 | ("r-a4core" ,r-a4core) |
| 4033 | ("r-a4preproc" ,r-a4preproc) |
| 4034 | ("r-a4reporting" ,r-a4reporting))) |
| 4035 | (home-page "https://bioconductor.org/packages/a4/") |
| 4036 | (synopsis "Automated Affymetrix array analysis umbrella package") |
| 4037 | (description |
| 4038 | "This package provides a software suite for the automated analysis of |
| 4039 | Affymetrix arrays.") |
| 4040 | (license license:gpl3))) |
| 4041 | |
| 4042 | (define-public r-abseqr |
| 4043 | (package |
| 4044 | (name "r-abseqr") |
| 4045 | (version "1.4.0") |
| 4046 | (source |
| 4047 | (origin |
| 4048 | (method url-fetch) |
| 4049 | (uri (bioconductor-uri "abseqR" version)) |
| 4050 | (sha256 |
| 4051 | (base32 |
| 4052 | "1n9h5qkj4njr1f8fvhg9sj9wxcd7hljnnk8m80zwswzs2n9ivppa")))) |
| 4053 | (properties `((upstream-name . "abseqR"))) |
| 4054 | (build-system r-build-system) |
| 4055 | (inputs |
| 4056 | `(("pandoc" ,ghc-pandoc))) |
| 4057 | (propagated-inputs |
| 4058 | `(("r-biocparallel" ,r-biocparallel) |
| 4059 | ("r-biocstyle" ,r-biocstyle) |
| 4060 | ("r-circlize" ,r-circlize) |
| 4061 | ("r-flexdashboard" ,r-flexdashboard) |
| 4062 | ("r-ggcorrplot" ,r-ggcorrplot) |
| 4063 | ("r-ggdendro" ,r-ggdendro) |
| 4064 | ("r-ggplot2" ,r-ggplot2) |
| 4065 | ("r-gridextra" ,r-gridextra) |
| 4066 | ("r-knitr" ,r-knitr) |
| 4067 | ("r-plotly" ,r-plotly) |
| 4068 | ("r-plyr" ,r-plyr) |
| 4069 | ("r-png" ,r-png) |
| 4070 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 4071 | ("r-reshape2" ,r-reshape2) |
| 4072 | ("r-rmarkdown" ,r-rmarkdown) |
| 4073 | ("r-stringr" ,r-stringr) |
| 4074 | ("r-vegan" ,r-vegan) |
| 4075 | ("r-venndiagram" ,r-venndiagram))) |
| 4076 | (home-page "https://github.com/malhamdoosh/abseqR") |
| 4077 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") |
| 4078 | (description |
| 4079 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of |
| 4080 | sequencing datasets generated from antibody libraries and abseqR is one of its |
| 4081 | packages. AbseqR empowers the users of abseqPy with plotting and reporting |
| 4082 | capabilities and allows them to generate interactive HTML reports for the |
| 4083 | convenience of viewing and sharing with other researchers. Additionally, |
| 4084 | abseqR extends abseqPy to compare multiple repertoire analyses and perform |
| 4085 | further downstream analysis on its output.") |
| 4086 | (license license:gpl3))) |
| 4087 | |
| 4088 | (define-public r-bacon |
| 4089 | (package |
| 4090 | (name "r-bacon") |
| 4091 | (version "1.14.0") |
| 4092 | (source |
| 4093 | (origin |
| 4094 | (method url-fetch) |
| 4095 | (uri (bioconductor-uri "bacon" version)) |
| 4096 | (sha256 |
| 4097 | (base32 |
| 4098 | "1q18vm4znl47v56cnvx9y5ygrial2mdjpl8x1043jq00kyygrc86")))) |
| 4099 | (build-system r-build-system) |
| 4100 | (propagated-inputs |
| 4101 | `(("r-biocparallel" ,r-biocparallel) |
| 4102 | ("r-ellipse" ,r-ellipse) |
| 4103 | ("r-ggplot2" ,r-ggplot2))) |
| 4104 | (native-inputs |
| 4105 | `(("r-knitr" ,r-knitr))) |
| 4106 | (home-page "https://bioconductor.org/packages/bacon/") |
| 4107 | (synopsis "Controlling bias and inflation in association studies") |
| 4108 | (description |
| 4109 | "Bacon can be used to remove inflation and bias often observed in |
| 4110 | epigenome- and transcriptome-wide association studies. To this end bacon |
| 4111 | constructs an empirical null distribution using a Gibbs Sampling algorithm by |
| 4112 | fitting a three-component normal mixture on z-scores.") |
| 4113 | (license license:gpl2+))) |
| 4114 | |
| 4115 | (define-public r-rgadem |
| 4116 | (package |
| 4117 | (name "r-rgadem") |
| 4118 | (version "2.34.1") |
| 4119 | (source |
| 4120 | (origin |
| 4121 | (method url-fetch) |
| 4122 | (uri (bioconductor-uri "rGADEM" version)) |
| 4123 | (sha256 |
| 4124 | (base32 |
| 4125 | "12xm4p4qsczf57kip8bvi6pr8sb5gvn11dnbz7lbh6sc03sx3q2h")))) |
| 4126 | (properties `((upstream-name . "rGADEM"))) |
| 4127 | (build-system r-build-system) |
| 4128 | (propagated-inputs |
| 4129 | `(("r-biostrings" ,r-biostrings) |
| 4130 | ("r-bsgenome" ,r-bsgenome) |
| 4131 | ("r-genomicranges" ,r-genomicranges) |
| 4132 | ("r-iranges" ,r-iranges) |
| 4133 | ("r-seqlogo" ,r-seqlogo))) |
| 4134 | (home-page "https://bioconductor.org/packages/rGADEM/") |
| 4135 | (synopsis "De novo sequence motif discovery") |
| 4136 | (description |
| 4137 | "rGADEM is an efficient de novo motif discovery tool for large-scale |
| 4138 | genomic sequence data.") |
| 4139 | (license license:artistic2.0))) |
| 4140 | |
| 4141 | (define-public r-motiv |
| 4142 | (package |
| 4143 | (name "r-motiv") |
| 4144 | (version "1.42.0") |
| 4145 | (source |
| 4146 | (origin |
| 4147 | (method url-fetch) |
| 4148 | (uri (bioconductor-uri "MotIV" version)) |
| 4149 | (sha256 |
| 4150 | (base32 |
| 4151 | "07k4rw4nhcn4sg43psv1h7qr064gws22m2yyr7x8sy3f1i1c954k")))) |
| 4152 | (properties `((upstream-name . "MotIV"))) |
| 4153 | (build-system r-build-system) |
| 4154 | (inputs |
| 4155 | `(("gsl" ,gsl))) |
| 4156 | (propagated-inputs |
| 4157 | `(("r-biocgenerics" ,r-biocgenerics) |
| 4158 | ("r-biostrings" ,r-biostrings) |
| 4159 | ("r-genomicranges" ,r-genomicranges) |
| 4160 | ("r-iranges" ,r-iranges) |
| 4161 | ("r-lattice" ,r-lattice) |
| 4162 | ("r-rgadem" ,r-rgadem) |
| 4163 | ("r-s4vectors" ,r-s4vectors))) |
| 4164 | (home-page "https://bioconductor.org/packages/MotIV/") |
| 4165 | (synopsis "Motif identification and validation") |
| 4166 | (description |
| 4167 | "This package is used for the identification and validation of sequence |
| 4168 | motifs. It makes use of STAMP for comparing a set of motifs to a given |
| 4169 | database (e.g. JASPAR). It can also be used to visualize motifs, motif |
| 4170 | distributions, modules and filter motifs.") |
| 4171 | (license license:gpl2))) |
| 4172 | |
| 4173 | (define-public r-motifdb |
| 4174 | (package |
| 4175 | (name "r-motifdb") |
| 4176 | (version "1.28.0") |
| 4177 | (source (origin |
| 4178 | (method url-fetch) |
| 4179 | (uri (bioconductor-uri "MotifDb" version)) |
| 4180 | (sha256 |
| 4181 | (base32 "0m5apkjlvdq9yhjdyds3hivfnkbm6f059hy2bkjhalrlhd2si2jc")))) |
| 4182 | (properties `((upstream-name . "MotifDb"))) |
| 4183 | (build-system r-build-system) |
| 4184 | (propagated-inputs |
| 4185 | `(("r-biocgenerics" ,r-biocgenerics) |
| 4186 | ("r-biostrings" ,r-biostrings) |
| 4187 | ("r-iranges" ,r-iranges) |
| 4188 | ("r-rtracklayer" ,r-rtracklayer) |
| 4189 | ("r-s4vectors" ,r-s4vectors) |
| 4190 | ("r-splitstackshape" ,r-splitstackshape))) |
| 4191 | (home-page "https://www.bioconductor.org/packages/MotifDb/") |
| 4192 | (synopsis "Annotated collection of protein-DNA binding sequence motifs") |
| 4193 | (description "This package provides more than 2000 annotated position |
| 4194 | frequency matrices from nine public sources, for multiple organisms.") |
| 4195 | (license license:artistic2.0))) |
| 4196 | |
| 4197 | (define-public r-motifbreakr |
| 4198 | (package |
| 4199 | (name "r-motifbreakr") |
| 4200 | (version "2.0.0") |
| 4201 | (source (origin |
| 4202 | (method url-fetch) |
| 4203 | (uri (bioconductor-uri "motifbreakR" version)) |
| 4204 | (sha256 |
| 4205 | (base32 "190z8gj393qdpq5wz7gph96k0l8c1j9wd0p0llscysvk5kr1hf9n")))) |
| 4206 | (properties `((upstream-name . "motifbreakR"))) |
| 4207 | (build-system r-build-system) |
| 4208 | (propagated-inputs |
| 4209 | `(("r-grimport" ,r-grimport) |
| 4210 | ("r-stringr" ,r-stringr) |
| 4211 | ("r-biocgenerics" ,r-biocgenerics) |
| 4212 | ("r-s4vectors" ,r-s4vectors) |
| 4213 | ("r-iranges" ,r-iranges) |
| 4214 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 4215 | ("r-genomicranges" ,r-genomicranges) |
| 4216 | ("r-biostrings" ,r-biostrings) |
| 4217 | ("r-bsgenome" ,r-bsgenome) |
| 4218 | ("r-rtracklayer" ,r-rtracklayer) |
| 4219 | ("r-variantannotation" ,r-variantannotation) |
| 4220 | ("r-biocparallel" ,r-biocparallel) |
| 4221 | ("r-motifstack" ,r-motifstack) |
| 4222 | ("r-gviz" ,r-gviz) |
| 4223 | ("r-matrixstats" ,r-matrixstats) |
| 4224 | ("r-tfmpvalue" ,r-tfmpvalue) |
| 4225 | ("r-motifdb" ,r-motifdb))) |
| 4226 | (home-page "https://www.bioconductor.org/packages/motifbreakR/") |
| 4227 | (synopsis "Predicting disruptiveness of single nucleotide polymorphisms") |
| 4228 | (description "This package allows biologists to judge in the first place |
| 4229 | whether the sequence surrounding the polymorphism is a good match, and in |
| 4230 | the second place how much information is gained or lost in one allele of |
| 4231 | the polymorphism relative to another. This package gives a choice of |
| 4232 | algorithms for interrogation of genomes with motifs from public sources: |
| 4233 | @enumerate |
| 4234 | @item a weighted-sum probability matrix; |
| 4235 | @item log-probabilities; |
| 4236 | @item weighted by relative entropy. |
| 4237 | @end enumerate |
| 4238 | |
| 4239 | This package can predict effects for novel or previously described variants in |
| 4240 | public databases, making it suitable for tasks beyond the scope of its original |
| 4241 | design. Lastly, it can be used to interrogate any genome curated within |
| 4242 | Bioconductor.") |
| 4243 | (license license:gpl2+))) |
| 4244 | |
| 4245 | (define-public r-motifstack |
| 4246 | (package |
| 4247 | (name "r-motifstack") |
| 4248 | (version "1.30.0") |
| 4249 | (source |
| 4250 | (origin |
| 4251 | (method url-fetch) |
| 4252 | (uri (bioconductor-uri "motifStack" version)) |
| 4253 | (sha256 |
| 4254 | (base32 |
| 4255 | "00rafqs1gqlcxlbsdn9qnq9xb7wjphiksb3hsx76viqjbjzi14wg")))) |
| 4256 | (properties `((upstream-name . "motifStack"))) |
| 4257 | (build-system r-build-system) |
| 4258 | (propagated-inputs |
| 4259 | `(("r-ade4" ,r-ade4) |
| 4260 | ("r-biostrings" ,r-biostrings) |
| 4261 | ("r-ggplot2" ,r-ggplot2) |
| 4262 | ("r-grimport2" ,r-grimport2) |
| 4263 | ("r-htmlwidgets" ,r-htmlwidgets) |
| 4264 | ("r-motiv" ,r-motiv) |
| 4265 | ("r-scales" ,r-scales) |
| 4266 | ("r-xml" ,r-xml))) |
| 4267 | (home-page "https://bioconductor.org/packages/motifStack/") |
| 4268 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") |
| 4269 | (description |
| 4270 | "The motifStack package is designed for graphic representation of |
| 4271 | multiple motifs with different similarity scores. It works with both DNA/RNA |
| 4272 | sequence motifs and amino acid sequence motifs. In addition, it provides the |
| 4273 | flexibility for users to customize the graphic parameters such as the font |
| 4274 | type and symbol colors.") |
| 4275 | (license license:gpl2+))) |
| 4276 | |
| 4277 | (define-public r-genomicscores |
| 4278 | (package |
| 4279 | (name "r-genomicscores") |
| 4280 | (version "1.10.0") |
| 4281 | (source |
| 4282 | (origin |
| 4283 | (method url-fetch) |
| 4284 | (uri (bioconductor-uri "GenomicScores" version)) |
| 4285 | (sha256 |
| 4286 | (base32 |
| 4287 | "175iaqv7npa11yw48vmqpgx0qqs3g44c3dsya7ccwd1lg97fznkj")))) |
| 4288 | (properties `((upstream-name . "GenomicScores"))) |
| 4289 | (build-system r-build-system) |
| 4290 | (propagated-inputs |
| 4291 | `(("r-annotationhub" ,r-annotationhub) |
| 4292 | ("r-biobase" ,r-biobase) |
| 4293 | ("r-biocgenerics" ,r-biocgenerics) |
| 4294 | ("r-biostrings" ,r-biostrings) |
| 4295 | ("r-bsgenome" ,r-bsgenome) |
| 4296 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 4297 | ("r-genomicranges" ,r-genomicranges) |
| 4298 | ("r-iranges" ,r-iranges) |
| 4299 | ("r-s4vectors" ,r-s4vectors) |
| 4300 | ("r-xml" ,r-xml))) |
| 4301 | (home-page "https://github.com/rcastelo/GenomicScores/") |
| 4302 | (synopsis "Work with genome-wide position-specific scores") |
| 4303 | (description |
| 4304 | "This package provides infrastructure to store and access genome-wide |
| 4305 | position-specific scores within R and Bioconductor.") |
| 4306 | (license license:artistic2.0))) |
| 4307 | |
| 4308 | (define-public r-atacseqqc |
| 4309 | (package |
| 4310 | (name "r-atacseqqc") |
| 4311 | (version "1.10.4") |
| 4312 | (source |
| 4313 | (origin |
| 4314 | (method url-fetch) |
| 4315 | (uri (bioconductor-uri "ATACseqQC" version)) |
| 4316 | (sha256 |
| 4317 | (base32 |
| 4318 | "1g07ni134cyl3jd9y19afip39kxddfgpm1jjm0rhrm7jgssp24in")))) |
| 4319 | (properties `((upstream-name . "ATACseqQC"))) |
| 4320 | (build-system r-build-system) |
| 4321 | (propagated-inputs |
| 4322 | `(("r-biocgenerics" ,r-biocgenerics) |
| 4323 | ("r-biostrings" ,r-biostrings) |
| 4324 | ("r-bsgenome" ,r-bsgenome) |
| 4325 | ("r-chippeakanno" ,r-chippeakanno) |
| 4326 | ("r-edger" ,r-edger) |
| 4327 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 4328 | ("r-genomicalignments" ,r-genomicalignments) |
| 4329 | ("r-genomicranges" ,r-genomicranges) |
| 4330 | ("r-genomicscores" ,r-genomicscores) |
| 4331 | ("r-iranges" ,r-iranges) |
| 4332 | ("r-kernsmooth" ,r-kernsmooth) |
| 4333 | ("r-limma" ,r-limma) |
| 4334 | ("r-motifstack" ,r-motifstack) |
| 4335 | ("r-preseqr" ,r-preseqr) |
| 4336 | ("r-randomforest" ,r-randomforest) |
| 4337 | ("r-rsamtools" ,r-rsamtools) |
| 4338 | ("r-rtracklayer" ,r-rtracklayer) |
| 4339 | ("r-s4vectors" ,r-s4vectors))) |
| 4340 | (native-inputs |
| 4341 | `(("r-knitr" ,r-knitr))) |
| 4342 | (home-page "https://bioconductor.org/packages/ATACseqQC/") |
| 4343 | (synopsis "ATAC-seq quality control") |
| 4344 | (description |
| 4345 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using |
| 4346 | sequencing, is a rapid and sensitive method for chromatin accessibility |
| 4347 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq |
| 4348 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly |
| 4349 | assess whether their ATAC-seq experiment is successful. It includes |
| 4350 | diagnostic plots of fragment size distribution, proportion of mitochondria |
| 4351 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor |
| 4352 | footprints.") |
| 4353 | (license license:gpl2+))) |
| 4354 | |
| 4355 | (define-public r-gofuncr |
| 4356 | (package |
| 4357 | (name "r-gofuncr") |
| 4358 | (version "1.6.1") |
| 4359 | (source |
| 4360 | (origin |
| 4361 | (method url-fetch) |
| 4362 | (uri (bioconductor-uri "GOfuncR" version)) |
| 4363 | (sha256 |
| 4364 | (base32 |
| 4365 | "1wk7ja6f5il8jx8v05ijzcs9pijp3b953h566ya66xp7dz5jg9rb")))) |
| 4366 | (properties `((upstream-name . "GOfuncR"))) |
| 4367 | (build-system r-build-system) |
| 4368 | (propagated-inputs |
| 4369 | `(("r-annotationdbi" ,r-annotationdbi) |
| 4370 | ("r-genomicranges" ,r-genomicranges) |
| 4371 | ("r-gtools" ,r-gtools) |
| 4372 | ("r-iranges" ,r-iranges) |
| 4373 | ("r-mapplots" ,r-mapplots) |
| 4374 | ("r-rcpp" ,r-rcpp) |
| 4375 | ("r-vioplot" ,r-vioplot))) |
| 4376 | (native-inputs |
| 4377 | `(("r-knitr" ,r-knitr))) |
| 4378 | (home-page "https://bioconductor.org/packages/GOfuncR/") |
| 4379 | (synopsis "Gene ontology enrichment using FUNC") |
| 4380 | (description |
| 4381 | "GOfuncR performs a gene ontology enrichment analysis based on the |
| 4382 | ontology enrichment software FUNC. GO-annotations are obtained from |
| 4383 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is |
| 4384 | included in the package and updated regularly. GOfuncR provides the standard |
| 4385 | candidate vs background enrichment analysis using the hypergeometric test, as |
| 4386 | well as three additional tests: |
| 4387 | |
| 4388 | @enumerate |
| 4389 | @item the Wilcoxon rank-sum test that is used when genes are ranked, |
| 4390 | @item a binomial test that is used when genes are associated with two counts, |
| 4391 | and |
| 4392 | @item a Chi-square or Fisher's exact test that is used in cases when genes are |
| 4393 | associated with four counts. |
| 4394 | @end enumerate |
| 4395 | |
| 4396 | To correct for multiple testing and interdependency of the tests, family-wise |
| 4397 | error rates are computed based on random permutations of the gene-associated |
| 4398 | variables. GOfuncR also provides tools for exploring the ontology graph and |
| 4399 | the annotations, and options to take gene-length or spatial clustering of |
| 4400 | genes into account. It is also possible to provide custom gene coordinates, |
| 4401 | annotations and ontologies.") |
| 4402 | (license license:gpl2+))) |
| 4403 | |
| 4404 | (define-public r-abaenrichment |
| 4405 | (package |
| 4406 | (name "r-abaenrichment") |
| 4407 | (version "1.16.0") |
| 4408 | (source |
| 4409 | (origin |
| 4410 | (method url-fetch) |
| 4411 | (uri (bioconductor-uri "ABAEnrichment" version)) |
| 4412 | (sha256 |
| 4413 | (base32 |
| 4414 | "128ik28j8kmdkycffhxajv5h174zdq9sfn2gz6ai90wgkdadbzwp")))) |
| 4415 | (properties `((upstream-name . "ABAEnrichment"))) |
| 4416 | (build-system r-build-system) |
| 4417 | (propagated-inputs |
| 4418 | `(("r-abadata" ,r-abadata) |
| 4419 | ("r-data-table" ,r-data-table) |
| 4420 | ("r-gofuncr" ,r-gofuncr) |
| 4421 | ("r-gplots" ,r-gplots) |
| 4422 | ("r-gtools" ,r-gtools) |
| 4423 | ("r-rcpp" ,r-rcpp))) |
| 4424 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") |
| 4425 | (synopsis "Gene expression enrichment in human brain regions") |
| 4426 | (description |
| 4427 | "The package ABAEnrichment is designed to test for enrichment of user |
| 4428 | defined candidate genes in the set of expressed genes in different human brain |
| 4429 | regions. The core function @code{aba_enrich} integrates the expression of the |
| 4430 | candidate gene set (averaged across donors) and the structural information of |
| 4431 | the brain using an ontology, both provided by the Allen Brain Atlas project.") |
| 4432 | (license license:gpl2+))) |
| 4433 | |
| 4434 | (define-public r-annotationfuncs |
| 4435 | (package |
| 4436 | (name "r-annotationfuncs") |
| 4437 | (version "1.36.0") |
| 4438 | (source |
| 4439 | (origin |
| 4440 | (method url-fetch) |
| 4441 | (uri (bioconductor-uri "AnnotationFuncs" version)) |
| 4442 | (sha256 |
| 4443 | (base32 |
| 4444 | "0ws14b1ibqml7w8kj0gi7wdp6wd8dcdpnrmcxldjzsyawf17q0yq")))) |
| 4445 | (properties |
| 4446 | `((upstream-name . "AnnotationFuncs"))) |
| 4447 | (build-system r-build-system) |
| 4448 | (propagated-inputs |
| 4449 | `(("r-annotationdbi" ,r-annotationdbi) |
| 4450 | ("r-dbi" ,r-dbi))) |
| 4451 | (home-page "https://www.iysik.com/r/annotationfuncs") |
| 4452 | (synopsis "Annotation translation functions") |
| 4453 | (description |
| 4454 | "This package provides functions for handling translating between |
| 4455 | different identifieres using the Biocore Data Team data-packages (e.g. |
| 4456 | @code{org.Bt.eg.db}).") |
| 4457 | (license license:gpl2))) |
| 4458 | |
| 4459 | (define-public r-annotationtools |
| 4460 | (package |
| 4461 | (name "r-annotationtools") |
| 4462 | (version "1.60.0") |
| 4463 | (source |
| 4464 | (origin |
| 4465 | (method url-fetch) |
| 4466 | (uri (bioconductor-uri "annotationTools" version)) |
| 4467 | (sha256 |
| 4468 | (base32 |
| 4469 | "1cq7ayq2swp2ahlphz74nh5mb869rgyyr0kkqy1mxyilk8k2g44i")))) |
| 4470 | (properties |
| 4471 | `((upstream-name . "annotationTools"))) |
| 4472 | (build-system r-build-system) |
| 4473 | (propagated-inputs `(("r-biobase" ,r-biobase))) |
| 4474 | (home-page "https://bioconductor.org/packages/annotationTools/") |
| 4475 | (synopsis "Annotate microarrays and perform gene expression analyses") |
| 4476 | (description |
| 4477 | "This package provides functions to annotate microarrays, find orthologs, |
| 4478 | and integrate heterogeneous gene expression profiles using annotation and |
| 4479 | other molecular biology information available as flat file database (plain |
| 4480 | text files).") |
| 4481 | ;; Any version of the GPL. |
| 4482 | (license (list license:gpl2+)))) |
| 4483 | |
| 4484 | (define-public r-allelicimbalance |
| 4485 | (package |
| 4486 | (name "r-allelicimbalance") |
| 4487 | (version "1.24.0") |
| 4488 | (source |
| 4489 | (origin |
| 4490 | (method url-fetch) |
| 4491 | (uri (bioconductor-uri "AllelicImbalance" version)) |
| 4492 | (sha256 |
| 4493 | (base32 |
| 4494 | "0vy8w7ii2qljsmq8lr21lygkcrsshc7syyqhadlbxyj3scgi7kyc")))) |
| 4495 | (properties |
| 4496 | `((upstream-name . "AllelicImbalance"))) |
| 4497 | (build-system r-build-system) |
| 4498 | (propagated-inputs |
| 4499 | `(("r-annotationdbi" ,r-annotationdbi) |
| 4500 | ("r-biocgenerics" ,r-biocgenerics) |
| 4501 | ("r-biostrings" ,r-biostrings) |
| 4502 | ("r-bsgenome" ,r-bsgenome) |
| 4503 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 4504 | ("r-genomicalignments" ,r-genomicalignments) |
| 4505 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 4506 | ("r-genomicranges" ,r-genomicranges) |
| 4507 | ("r-gridextra" ,r-gridextra) |
| 4508 | ("r-gviz" ,r-gviz) |
| 4509 | ("r-iranges" ,r-iranges) |
| 4510 | ("r-lattice" ,r-lattice) |
| 4511 | ("r-latticeextra" ,r-latticeextra) |
| 4512 | ("r-nlme" ,r-nlme) |
| 4513 | ("r-rsamtools" ,r-rsamtools) |
| 4514 | ("r-s4vectors" ,r-s4vectors) |
| 4515 | ("r-seqinr" ,r-seqinr) |
| 4516 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 4517 | ("r-variantannotation" ,r-variantannotation))) |
| 4518 | (home-page "https://github.com/pappewaio/AllelicImbalance") |
| 4519 | (synopsis "Investigate allele-specific expression") |
| 4520 | (description |
| 4521 | "This package provides a framework for allele-specific expression |
| 4522 | investigation using RNA-seq data.") |
| 4523 | (license license:gpl3))) |
| 4524 | |
| 4525 | (define-public r-aucell |
| 4526 | (package |
| 4527 | (name "r-aucell") |
| 4528 | (version "1.8.0") |
| 4529 | (source |
| 4530 | (origin |
| 4531 | (method url-fetch) |
| 4532 | (uri (bioconductor-uri "AUCell" version)) |
| 4533 | (sha256 |
| 4534 | (base32 |
| 4535 | "1g4mdq8z29fjxrfjng0fb3cvbph49mwds4ijsa2bn2k6f75dnzky")))) |
| 4536 | (properties `((upstream-name . "AUCell"))) |
| 4537 | (build-system r-build-system) |
| 4538 | (propagated-inputs |
| 4539 | `(("r-biocgenerics" ,r-biocgenerics) |
| 4540 | ("r-data-table" ,r-data-table) |
| 4541 | ("r-gseabase" ,r-gseabase) |
| 4542 | ("r-mixtools" ,r-mixtools) |
| 4543 | ("r-r-utils" ,r-r-utils) |
| 4544 | ("r-s4vectors" ,r-s4vectors) |
| 4545 | ("r-shiny" ,r-shiny) |
| 4546 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 4547 | (home-page "https://bioconductor.org/packages/AUCell/") |
| 4548 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") |
| 4549 | (description |
| 4550 | "AUCell identifies cells with active gene sets (e.g. signatures, |
| 4551 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area |
| 4552 | Under the Curve} (AUC) to calculate whether a critical subset of the input |
| 4553 | gene set is enriched within the expressed genes for each cell. The |
| 4554 | distribution of AUC scores across all the cells allows exploring the relative |
| 4555 | expression of the signature. Since the scoring method is ranking-based, |
| 4556 | AUCell is independent of the gene expression units and the normalization |
| 4557 | procedure. In addition, since the cells are evaluated individually, it can |
| 4558 | easily be applied to bigger datasets, subsetting the expression matrix if |
| 4559 | needed.") |
| 4560 | (license license:gpl3))) |
| 4561 | |
| 4562 | (define-public r-ebimage |
| 4563 | (package |
| 4564 | (name "r-ebimage") |
| 4565 | (version "4.28.1") |
| 4566 | (source |
| 4567 | (origin |
| 4568 | (method url-fetch) |
| 4569 | (uri (bioconductor-uri "EBImage" version)) |
| 4570 | (sha256 |
| 4571 | (base32 |
| 4572 | "0q54q2nw6p1s4nrj1l8qz78m67xcysj2x82zs43my8iv2g9iifgs")))) |
| 4573 | (properties `((upstream-name . "EBImage"))) |
| 4574 | (build-system r-build-system) |
| 4575 | (propagated-inputs |
| 4576 | `(("r-abind" ,r-abind) |
| 4577 | ("r-biocgenerics" ,r-biocgenerics) |
| 4578 | ("r-fftwtools" ,r-fftwtools) |
| 4579 | ("r-htmltools" ,r-htmltools) |
| 4580 | ("r-htmlwidgets" ,r-htmlwidgets) |
| 4581 | ("r-jpeg" ,r-jpeg) |
| 4582 | ("r-locfit" ,r-locfit) |
| 4583 | ("r-png" ,r-png) |
| 4584 | ("r-rcurl" ,r-rcurl) |
| 4585 | ("r-tiff" ,r-tiff))) |
| 4586 | (native-inputs |
| 4587 | `(("r-knitr" ,r-knitr))) ; for vignettes |
| 4588 | (home-page "https://github.com/aoles/EBImage") |
| 4589 | (synopsis "Image processing and analysis toolbox for R") |
| 4590 | (description |
| 4591 | "EBImage provides general purpose functionality for image processing and |
| 4592 | analysis. In the context of (high-throughput) microscopy-based cellular |
| 4593 | assays, EBImage offers tools to segment cells and extract quantitative |
| 4594 | cellular descriptors. This allows the automation of such tasks using the R |
| 4595 | programming language and facilitates the use of other tools in the R |
| 4596 | environment for signal processing, statistical modeling, machine learning and |
| 4597 | visualization with image data.") |
| 4598 | ;; Any version of the LGPL. |
| 4599 | (license license:lgpl2.1+))) |
| 4600 | |
| 4601 | (define-public r-yamss |
| 4602 | (package |
| 4603 | (name "r-yamss") |
| 4604 | (version "1.12.1") |
| 4605 | (source |
| 4606 | (origin |
| 4607 | (method url-fetch) |
| 4608 | (uri (bioconductor-uri "yamss" version)) |
| 4609 | (sha256 |
| 4610 | (base32 |
| 4611 | "12jr7hbrwhb1gfjadj1024hv80ra22miy46dn40nmsrbklkfn3rw")))) |
| 4612 | (build-system r-build-system) |
| 4613 | (propagated-inputs |
| 4614 | `(("r-biocgenerics" ,r-biocgenerics) |
| 4615 | ("r-data-table" ,r-data-table) |
| 4616 | ("r-ebimage" ,r-ebimage) |
| 4617 | ("r-iranges" ,r-iranges) |
| 4618 | ("r-limma" ,r-limma) |
| 4619 | ("r-matrix" ,r-matrix) |
| 4620 | ("r-mzr" ,r-mzr) |
| 4621 | ("r-s4vectors" ,r-s4vectors) |
| 4622 | ("r-summarizedexperiment" |
| 4623 | ,r-summarizedexperiment))) |
| 4624 | (home-page "https://github.com/hansenlab/yamss") |
| 4625 | (synopsis "Tools for high-throughput metabolomics") |
| 4626 | (description |
| 4627 | "This package provides tools to analyze and visualize high-throughput |
| 4628 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
| 4629 | preprocess data in a way that enables reliable and powerful differential |
| 4630 | analysis.") |
| 4631 | (license license:artistic2.0))) |
| 4632 | |
| 4633 | (define-public r-gtrellis |
| 4634 | (package |
| 4635 | (name "r-gtrellis") |
| 4636 | (version "1.18.0") |
| 4637 | (source |
| 4638 | (origin |
| 4639 | (method url-fetch) |
| 4640 | (uri (bioconductor-uri "gtrellis" version)) |
| 4641 | (sha256 |
| 4642 | (base32 |
| 4643 | "0mgspmv6p1a2k98jyy2dfl0wpa2vh7bhnjfm2xaqmcsxzmbjhh9z")))) |
| 4644 | (build-system r-build-system) |
| 4645 | (propagated-inputs |
| 4646 | `(("r-circlize" ,r-circlize) |
| 4647 | ("r-genomicranges" ,r-genomicranges) |
| 4648 | ("r-getoptlong" ,r-getoptlong) |
| 4649 | ("r-iranges" ,r-iranges))) |
| 4650 | (home-page "https://github.com/jokergoo/gtrellis") |
| 4651 | (synopsis "Genome level Trellis layout") |
| 4652 | (description |
| 4653 | "Genome level Trellis graph visualizes genomic data conditioned by |
| 4654 | genomic categories (e.g. chromosomes). For each genomic category, multiple |
| 4655 | dimensional data which are represented as tracks describe different features |
| 4656 | from different aspects. This package provides high flexibility to arrange |
| 4657 | genomic categories and to add self-defined graphics in the plot.") |
| 4658 | (license license:expat))) |
| 4659 | |
| 4660 | (define-public r-somaticsignatures |
| 4661 | (package |
| 4662 | (name "r-somaticsignatures") |
| 4663 | (version "2.22.0") |
| 4664 | (source |
| 4665 | (origin |
| 4666 | (method url-fetch) |
| 4667 | (uri (bioconductor-uri "SomaticSignatures" version)) |
| 4668 | (sha256 |
| 4669 | (base32 |
| 4670 | "1gvrkahllwz38g3hn9pjlikhfqz19a4qglcqmyrxk7h9ybx5zy5z")))) |
| 4671 | (properties |
| 4672 | `((upstream-name . "SomaticSignatures"))) |
| 4673 | (build-system r-build-system) |
| 4674 | (propagated-inputs |
| 4675 | `(("r-biobase" ,r-biobase) |
| 4676 | ("r-biostrings" ,r-biostrings) |
| 4677 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 4678 | ("r-genomicranges" ,r-genomicranges) |
| 4679 | ("r-ggbio" ,r-ggbio) |
| 4680 | ("r-ggplot2" ,r-ggplot2) |
| 4681 | ("r-iranges" ,r-iranges) |
| 4682 | ("r-nmf" ,r-nmf) |
| 4683 | ("r-pcamethods" ,r-pcamethods) |
| 4684 | ("r-proxy" ,r-proxy) |
| 4685 | ("r-reshape2" ,r-reshape2) |
| 4686 | ("r-s4vectors" ,r-s4vectors) |
| 4687 | ("r-variantannotation" ,r-variantannotation))) |
| 4688 | (home-page "https://github.com/juliangehring/SomaticSignatures") |
| 4689 | (synopsis "Somatic signatures") |
| 4690 | (description |
| 4691 | "This package identifies mutational signatures of @dfn{single nucleotide |
| 4692 | variants} (SNVs). It provides a infrastructure related to the methodology |
| 4693 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix |
| 4694 | decomposition algorithms.") |
| 4695 | (license license:expat))) |
| 4696 | |
| 4697 | (define-public r-yapsa |
| 4698 | (package |
| 4699 | (name "r-yapsa") |
| 4700 | (version "1.12.0") |
| 4701 | (source |
| 4702 | (origin |
| 4703 | (method url-fetch) |
| 4704 | (uri (bioconductor-uri "YAPSA" version)) |
| 4705 | (sha256 |
| 4706 | (base32 |
| 4707 | "132x51f8k8zyx6j8jk05x4lr9q1hlblgvr69wkhn0q3f8mhaj926")))) |
| 4708 | (properties `((upstream-name . "YAPSA"))) |
| 4709 | (build-system r-build-system) |
| 4710 | (propagated-inputs |
| 4711 | `(("r-circlize" ,r-circlize) |
| 4712 | ("r-complexheatmap" ,r-complexheatmap) |
| 4713 | ("r-corrplot" ,r-corrplot) |
| 4714 | ("r-dendextend" ,r-dendextend) |
| 4715 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 4716 | ("r-genomicranges" ,r-genomicranges) |
| 4717 | ("r-getoptlong" ,r-getoptlong) |
| 4718 | ("r-ggplot2" ,r-ggplot2) |
| 4719 | ("r-gridextra" ,r-gridextra) |
| 4720 | ("r-gtrellis" ,r-gtrellis) |
| 4721 | ("r-keggrest" ,r-keggrest) |
| 4722 | ("r-lsei" ,r-lsei) |
| 4723 | ("r-pmcmr" ,r-pmcmr) |
| 4724 | ("r-reshape2" ,r-reshape2) |
| 4725 | ("r-somaticsignatures" ,r-somaticsignatures) |
| 4726 | ("r-variantannotation" ,r-variantannotation))) |
| 4727 | (home-page "https://bioconductor.org/packages/YAPSA/") |
| 4728 | (synopsis "Yet another package for signature analysis") |
| 4729 | (description |
| 4730 | "This package provides functions and routines useful in the analysis of |
| 4731 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, |
| 4732 | functions to perform a signature analysis with known signatures and a |
| 4733 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are |
| 4734 | provided.") |
| 4735 | (license license:gpl3))) |
| 4736 | |
| 4737 | (define-public r-gcrma |
| 4738 | (package |
| 4739 | (name "r-gcrma") |
| 4740 | (version "2.58.0") |
| 4741 | (source |
| 4742 | (origin |
| 4743 | (method url-fetch) |
| 4744 | (uri (bioconductor-uri "gcrma" version)) |
| 4745 | (sha256 |
| 4746 | (base32 |
| 4747 | "0c9sa9ldlcpdcjdan8m4ndnyaisr6wbarq486sl44ikh7wf1csfx")))) |
| 4748 | (build-system r-build-system) |
| 4749 | (propagated-inputs |
| 4750 | `(("r-affy" ,r-affy) |
| 4751 | ("r-affyio" ,r-affyio) |
| 4752 | ("r-biobase" ,r-biobase) |
| 4753 | ("r-biocmanager" ,r-biocmanager) |
| 4754 | ("r-biostrings" ,r-biostrings) |
| 4755 | ("r-xvector" ,r-xvector))) |
| 4756 | (home-page "https://bioconductor.org/packages/gcrma/") |
| 4757 | (synopsis "Background adjustment using sequence information") |
| 4758 | (description |
| 4759 | "Gcrma adjusts for background intensities in Affymetrix array data which |
| 4760 | include optical noise and @dfn{non-specific binding} (NSB). The main function |
| 4761 | @code{gcrma} converts background adjusted probe intensities to expression |
| 4762 | measures using the same normalization and summarization methods as a |
| 4763 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information |
| 4764 | to estimate probe affinity to NSB. The sequence information is summarized in |
| 4765 | a more complex way than the simple GC content. Instead, the base types (A, T, |
| 4766 | G or C) at each position along the probe determine the affinity of each probe. |
| 4767 | The parameters of the position-specific base contributions to the probe |
| 4768 | affinity is estimated in an NSB experiment in which only NSB but no |
| 4769 | gene-specific bidning is expected.") |
| 4770 | ;; Any version of the LGPL |
| 4771 | (license license:lgpl2.1+))) |
| 4772 | |
| 4773 | (define-public r-simpleaffy |
| 4774 | (package |
| 4775 | (name "r-simpleaffy") |
| 4776 | (version "2.62.0") |
| 4777 | (source |
| 4778 | (origin |
| 4779 | (method url-fetch) |
| 4780 | (uri (bioconductor-uri "simpleaffy" version)) |
| 4781 | (sha256 |
| 4782 | (base32 |
| 4783 | "18bz3pfgp0f7906flrljx97ann8s71pnb8gpw7nah46n8vqc0xcs")))) |
| 4784 | (build-system r-build-system) |
| 4785 | (propagated-inputs |
| 4786 | `(("r-affy" ,r-affy) |
| 4787 | ("r-biobase" ,r-biobase) |
| 4788 | ("r-biocgenerics" ,r-biocgenerics) |
| 4789 | ("r-gcrma" ,r-gcrma) |
| 4790 | ("r-genefilter" ,r-genefilter))) |
| 4791 | (home-page "https://bioconductor.org/packages/simpleaffy/") |
| 4792 | (synopsis "Very simple high level analysis of Affymetrix data") |
| 4793 | (description |
| 4794 | "This package provides high level functions for reading Affy @file{.CEL} |
| 4795 | files, phenotypic data, and then computing simple things with it, such as |
| 4796 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} |
| 4797 | library. It also has some basic scatter plot functions and mechanisms for |
| 4798 | generating high resolution journal figures.") |
| 4799 | (license license:gpl2+))) |
| 4800 | |
| 4801 | (define-public r-yaqcaffy |
| 4802 | (package |
| 4803 | (name "r-yaqcaffy") |
| 4804 | (version "1.46.0") |
| 4805 | (source |
| 4806 | (origin |
| 4807 | (method url-fetch) |
| 4808 | (uri (bioconductor-uri "yaqcaffy" version)) |
| 4809 | (sha256 |
| 4810 | (base32 |
| 4811 | "0kzzqsf1lfbcmy95w2z0c9qrvp7mbwm50k2l9wvz3xa5wz6xa7gz")))) |
| 4812 | (build-system r-build-system) |
| 4813 | (propagated-inputs |
| 4814 | `(("r-simpleaffy" ,r-simpleaffy))) |
| 4815 | (home-page "https://bioconductor.org/packages/yaqcaffy/") |
| 4816 | (synopsis "Affymetrix quality control and reproducibility analysis") |
| 4817 | (description |
| 4818 | "This is a package that can be used for quality control of Affymetrix |
| 4819 | GeneChip expression data and reproducibility analysis of human whole genome |
| 4820 | chips with the MAQC reference datasets.") |
| 4821 | (license license:artistic2.0))) |
| 4822 | |
| 4823 | (define-public r-quantro |
| 4824 | (package |
| 4825 | (name "r-quantro") |
| 4826 | (version "1.20.0") |
| 4827 | (source |
| 4828 | (origin |
| 4829 | (method url-fetch) |
| 4830 | (uri (bioconductor-uri "quantro" version)) |
| 4831 | (sha256 |
| 4832 | (base32 |
| 4833 | "09f3x1j50ll5hhn3qwys5x06mii3fqsrk6dkvsxai0kdxv9cjz9m")))) |
| 4834 | (build-system r-build-system) |
| 4835 | (propagated-inputs |
| 4836 | `(("r-biobase" ,r-biobase) |
| 4837 | ("r-doparallel" ,r-doparallel) |
| 4838 | ("r-foreach" ,r-foreach) |
| 4839 | ("r-ggplot2" ,r-ggplot2) |
| 4840 | ("r-iterators" ,r-iterators) |
| 4841 | ("r-minfi" ,r-minfi) |
| 4842 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 4843 | (home-page "https://bioconductor.org/packages/quantro/") |
| 4844 | (synopsis "Test for when to use quantile normalization") |
| 4845 | (description |
| 4846 | "This package provides a data-driven test for the assumptions of quantile |
| 4847 | normalization using raw data such as objects that inherit eSets (e.g. |
| 4848 | ExpressionSet, MethylSet). Group level information about each sample (such as |
| 4849 | Tumor / Normal status) must also be provided because the test assesses if |
| 4850 | there are global differences in the distributions between the user-defined |
| 4851 | groups.") |
| 4852 | (license license:gpl3+))) |
| 4853 | |
| 4854 | (define-public r-yarn |
| 4855 | (package |
| 4856 | (name "r-yarn") |
| 4857 | (version "1.12.0") |
| 4858 | (source |
| 4859 | (origin |
| 4860 | (method url-fetch) |
| 4861 | (uri (bioconductor-uri "yarn" version)) |
| 4862 | (sha256 |
| 4863 | (base32 |
| 4864 | "0891a10adkhm1zpm7fpcxc2xfxjf9yrpckaz87b2wdjdiwivc4cp")))) |
| 4865 | (build-system r-build-system) |
| 4866 | (propagated-inputs |
| 4867 | `(("r-biobase" ,r-biobase) |
| 4868 | ("r-biomart" ,r-biomart) |
| 4869 | ("r-downloader" ,r-downloader) |
| 4870 | ("r-edger" ,r-edger) |
| 4871 | ("r-gplots" ,r-gplots) |
| 4872 | ("r-limma" ,r-limma) |
| 4873 | ("r-matrixstats" ,r-matrixstats) |
| 4874 | ("r-preprocesscore" ,r-preprocesscore) |
| 4875 | ("r-quantro" ,r-quantro) |
| 4876 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 4877 | ("r-readr" ,r-readr))) |
| 4878 | (home-page "https://bioconductor.org/packages/yarn/") |
| 4879 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") |
| 4880 | (description |
| 4881 | "Expedite large RNA-Seq analyses using a combination of previously |
| 4882 | developed tools. YARN is meant to make it easier for the user in performing |
| 4883 | basic mis-annotation quality control, filtering, and condition-aware |
| 4884 | normalization. YARN leverages many Bioconductor tools and statistical |
| 4885 | techniques to account for the large heterogeneity and sparsity found in very |
| 4886 | large RNA-seq experiments.") |
| 4887 | (license license:artistic2.0))) |
| 4888 | |
| 4889 | (define-public r-roar |
| 4890 | (package |
| 4891 | (name "r-roar") |
| 4892 | (version "1.22.0") |
| 4893 | (source |
| 4894 | (origin |
| 4895 | (method url-fetch) |
| 4896 | (uri (bioconductor-uri "roar" version)) |
| 4897 | (sha256 |
| 4898 | (base32 |
| 4899 | "1nqw0agx9x8ycdf0gw17fdlnmzpw9x3zig1wcy10xpyhyjdbbi06")))) |
| 4900 | (build-system r-build-system) |
| 4901 | (propagated-inputs |
| 4902 | `(("r-biocgenerics" ,r-biocgenerics) |
| 4903 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 4904 | ("r-genomicalignments" ,r-genomicalignments) |
| 4905 | ("r-genomicranges" ,r-genomicranges) |
| 4906 | ("r-iranges" ,r-iranges) |
| 4907 | ("r-rtracklayer" ,r-rtracklayer) |
| 4908 | ("r-s4vectors" ,r-s4vectors) |
| 4909 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 4910 | (home-page "https://github.com/vodkatad/roar/") |
| 4911 | (synopsis "Identify differential APA usage from RNA-seq alignments") |
| 4912 | (description |
| 4913 | "This package provides tools for identifying preferential usage of APA |
| 4914 | sites, comparing two biological conditions, starting from known alternative |
| 4915 | sites and alignments obtained from standard RNA-seq experiments.") |
| 4916 | (license license:gpl3))) |
| 4917 | |
| 4918 | (define-public r-xbseq |
| 4919 | (package |
| 4920 | (name "r-xbseq") |
| 4921 | (version "1.18.0") |
| 4922 | (source |
| 4923 | (origin |
| 4924 | (method url-fetch) |
| 4925 | (uri (bioconductor-uri "XBSeq" version)) |
| 4926 | (sha256 |
| 4927 | (base32 |
| 4928 | "1qr5gvf8jcx6r0ac7d2wmnikswmp3k71lirnw7dyr6fndzrdz9lp")))) |
| 4929 | (properties `((upstream-name . "XBSeq"))) |
| 4930 | (build-system r-build-system) |
| 4931 | (propagated-inputs |
| 4932 | `(("r-biobase" ,r-biobase) |
| 4933 | ("r-deseq2" ,r-deseq2) |
| 4934 | ("r-dplyr" ,r-dplyr) |
| 4935 | ("r-ggplot2" ,r-ggplot2) |
| 4936 | ("r-locfit" ,r-locfit) |
| 4937 | ("r-magrittr" ,r-magrittr) |
| 4938 | ("r-matrixstats" ,r-matrixstats) |
| 4939 | ("r-pracma" ,r-pracma) |
| 4940 | ("r-roar" ,r-roar))) |
| 4941 | (home-page "https://github.com/Liuy12/XBSeq") |
| 4942 | (synopsis "Test for differential expression for RNA-seq data") |
| 4943 | (description |
| 4944 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential |
| 4945 | expression} (DE), where a statistical model was established based on the |
| 4946 | assumption that observed signals are the convolution of true expression |
| 4947 | signals and sequencing noises. The mapped reads in non-exonic regions are |
| 4948 | considered as sequencing noises, which follows a Poisson distribution. Given |
| 4949 | measurable observed signal and background noise from RNA-seq data, true |
| 4950 | expression signals, assuming governed by the negative binomial distribution, |
| 4951 | can be delineated and thus the accurate detection of differential expressed |
| 4952 | genes.") |
| 4953 | (license license:gpl3+))) |
| 4954 | |
| 4955 | (define-public r-massspecwavelet |
| 4956 | (package |
| 4957 | (name "r-massspecwavelet") |
| 4958 | (version "1.52.0") |
| 4959 | (source |
| 4960 | (origin |
| 4961 | (method url-fetch) |
| 4962 | (uri (bioconductor-uri "MassSpecWavelet" version)) |
| 4963 | (sha256 |
| 4964 | (base32 |
| 4965 | "0xnj3ncrwvr2b8msi3g77mgzj0zaksn3lgqdn1abh0ww5wgk83v7")))) |
| 4966 | (properties |
| 4967 | `((upstream-name . "MassSpecWavelet"))) |
| 4968 | (build-system r-build-system) |
| 4969 | (propagated-inputs |
| 4970 | `(("r-waveslim" ,r-waveslim))) |
| 4971 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") |
| 4972 | (synopsis "Mass spectrum processing by wavelet-based algorithms") |
| 4973 | (description |
| 4974 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) |
| 4975 | data mainly through the use of wavelet transforms. It supports peak detection |
| 4976 | based on @dfn{Continuous Wavelet Transform} (CWT).") |
| 4977 | (license license:lgpl2.0+))) |
| 4978 | |
| 4979 | (define-public r-xcms |
| 4980 | (package |
| 4981 | (name "r-xcms") |
| 4982 | (version "3.8.2") |
| 4983 | (source |
| 4984 | (origin |
| 4985 | (method url-fetch) |
| 4986 | (uri (bioconductor-uri "xcms" version)) |
| 4987 | (sha256 |
| 4988 | (base32 |
| 4989 | "0bfl56v3l6k31i11l09nx1yqfjy6z5yragm6k83z4w0mpgk18y7g")))) |
| 4990 | (build-system r-build-system) |
| 4991 | (propagated-inputs |
| 4992 | `(("r-biobase" ,r-biobase) |
| 4993 | ("r-biocgenerics" ,r-biocgenerics) |
| 4994 | ("r-biocparallel" ,r-biocparallel) |
| 4995 | ("r-iranges" ,r-iranges) |
| 4996 | ("r-lattice" ,r-lattice) |
| 4997 | ("r-massspecwavelet" ,r-massspecwavelet) |
| 4998 | ("r-msnbase" ,r-msnbase) |
| 4999 | ("r-multtest" ,r-multtest) |
| 5000 | ("r-mzr" ,r-mzr) |
| 5001 | ("r-plyr" ,r-plyr) |
| 5002 | ("r-protgenerics" ,r-protgenerics) |
| 5003 | ("r-rann" ,r-rann) |
| 5004 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 5005 | ("r-robustbase" ,r-robustbase) |
| 5006 | ("r-s4vectors" ,r-s4vectors))) |
| 5007 | (home-page "https://bioconductor.org/packages/xcms/") |
| 5008 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") |
| 5009 | (description |
| 5010 | "This package provides a framework for processing and visualization of |
| 5011 | chromatographically separated and single-spectra mass spectral data. It |
| 5012 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses |
| 5013 | data for high-throughput, untargeted analyte profiling.") |
| 5014 | (license license:gpl2+))) |
| 5015 | |
| 5016 | (define-public r-wrench |
| 5017 | (package |
| 5018 | (name "r-wrench") |
| 5019 | (version "1.4.0") |
| 5020 | (source |
| 5021 | (origin |
| 5022 | (method url-fetch) |
| 5023 | (uri (bioconductor-uri "Wrench" version)) |
| 5024 | (sha256 |
| 5025 | (base32 |
| 5026 | "1s8d7jn0dk5zk2fhvsd4sgicypz4c41nzf19nqzcwb9bd6asgrwm")))) |
| 5027 | (properties `((upstream-name . "Wrench"))) |
| 5028 | (build-system r-build-system) |
| 5029 | (propagated-inputs |
| 5030 | `(("r-limma" ,r-limma) |
| 5031 | ("r-locfit" ,r-locfit) |
| 5032 | ("r-matrixstats" ,r-matrixstats))) |
| 5033 | (home-page "https://github.com/HCBravoLab/Wrench") |
| 5034 | (synopsis "Wrench normalization for sparse count data") |
| 5035 | (description |
| 5036 | "Wrench is a package for normalization sparse genomic count data, like |
| 5037 | that arising from 16s metagenomic surveys.") |
| 5038 | (license license:artistic2.0))) |
| 5039 | |
| 5040 | (define-public r-wiggleplotr |
| 5041 | (package |
| 5042 | (name "r-wiggleplotr") |
| 5043 | (version "1.10.1") |
| 5044 | (source |
| 5045 | (origin |
| 5046 | (method url-fetch) |
| 5047 | (uri (bioconductor-uri "wiggleplotr" version)) |
| 5048 | (sha256 |
| 5049 | (base32 |
| 5050 | "1pj2bsn5azs18mp5hr4g7c6rnds2y2rjjnak2785kaj7xi8jly4m")))) |
| 5051 | (build-system r-build-system) |
| 5052 | (propagated-inputs |
| 5053 | `(("r-assertthat" ,r-assertthat) |
| 5054 | ("r-cowplot" ,r-cowplot) |
| 5055 | ("r-dplyr" ,r-dplyr) |
| 5056 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 5057 | ("r-genomicranges" ,r-genomicranges) |
| 5058 | ("r-ggplot2" ,r-ggplot2) |
| 5059 | ("r-iranges" ,r-iranges) |
| 5060 | ("r-purrr" ,r-purrr) |
| 5061 | ("r-rtracklayer" ,r-rtracklayer) |
| 5062 | ("r-s4vectors" ,r-s4vectors))) |
| 5063 | (home-page "https://bioconductor.org/packages/wiggleplotr/") |
| 5064 | (synopsis "Make read coverage plots from BigWig files") |
| 5065 | (description |
| 5066 | "This package provides tools to visualize read coverage from sequencing |
| 5067 | experiments together with genomic annotations (genes, transcripts, peaks). |
| 5068 | Introns of long transcripts can be rescaled to a fixed length for better |
| 5069 | visualization of exonic read coverage.") |
| 5070 | (license license:asl2.0))) |
| 5071 | |
| 5072 | (define-public r-widgettools |
| 5073 | (package |
| 5074 | (name "r-widgettools") |
| 5075 | (version "1.64.0") |
| 5076 | (source |
| 5077 | (origin |
| 5078 | (method url-fetch) |
| 5079 | (uri (bioconductor-uri "widgetTools" version)) |
| 5080 | (sha256 |
| 5081 | (base32 |
| 5082 | "1nqy3icayacv5mlv5s5xgfli0dqzancs6zpffrl5p237c994nyr5")))) |
| 5083 | (properties `((upstream-name . "widgetTools"))) |
| 5084 | (build-system r-build-system) |
| 5085 | (home-page "https://bioconductor.org/packages/widgetTools/") |
| 5086 | (synopsis "Tools for creating interactive tcltk widgets") |
| 5087 | (description |
| 5088 | "This package contains tools to support the construction of tcltk |
| 5089 | widgets in R.") |
| 5090 | ;; Any version of the LGPL. |
| 5091 | (license license:lgpl3+))) |
| 5092 | |
| 5093 | (define-public r-webbioc |
| 5094 | (package |
| 5095 | (name "r-webbioc") |
| 5096 | (version "1.58.0") |
| 5097 | (source |
| 5098 | (origin |
| 5099 | (method url-fetch) |
| 5100 | (uri (bioconductor-uri "webbioc" version)) |
| 5101 | (sha256 |
| 5102 | (base32 |
| 5103 | "1cwrmvh1l603k6j1r425c4vrqp0zf0x7bgx7y1wnbq4r7yc5sp62")))) |
| 5104 | (build-system r-build-system) |
| 5105 | (inputs |
| 5106 | `(("netpbm" ,netpbm) |
| 5107 | ("perl" ,perl))) |
| 5108 | (propagated-inputs |
| 5109 | `(("r-affy" ,r-affy) |
| 5110 | ("r-annaffy" ,r-annaffy) |
| 5111 | ("r-biobase" ,r-biobase) |
| 5112 | ("r-biocmanager" ,r-biocmanager) |
| 5113 | ("r-gcrma" ,r-gcrma) |
| 5114 | ("r-multtest" ,r-multtest) |
| 5115 | ("r-qvalue" ,r-qvalue) |
| 5116 | ("r-vsn" ,r-vsn))) |
| 5117 | (home-page "https://www.bioconductor.org/") |
| 5118 | (synopsis "Bioconductor web interface") |
| 5119 | (description |
| 5120 | "This package provides an integrated web interface for doing microarray |
| 5121 | analysis using several of the Bioconductor packages. It is intended to be |
| 5122 | deployed as a centralized bioinformatics resource for use by many users. |
| 5123 | Currently only Affymetrix oligonucleotide analysis is supported.") |
| 5124 | (license license:gpl2+))) |
| 5125 | |
| 5126 | (define-public r-zfpkm |
| 5127 | (package |
| 5128 | (name "r-zfpkm") |
| 5129 | (version "1.8.0") |
| 5130 | (source |
| 5131 | (origin |
| 5132 | (method url-fetch) |
| 5133 | (uri (bioconductor-uri "zFPKM" version)) |
| 5134 | (sha256 |
| 5135 | (base32 |
| 5136 | "1hg0vc0ns8d4jpddn1v5a5m13a033b0wf1al01pb1lvmx5mzzr2n")))) |
| 5137 | (properties `((upstream-name . "zFPKM"))) |
| 5138 | (build-system r-build-system) |
| 5139 | (propagated-inputs |
| 5140 | `(("r-checkmate" ,r-checkmate) |
| 5141 | ("r-dplyr" ,r-dplyr) |
| 5142 | ("r-ggplot2" ,r-ggplot2) |
| 5143 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 5144 | ("r-tidyr" ,r-tidyr))) |
| 5145 | (home-page "https://github.com/ronammar/zFPKM/") |
| 5146 | (synopsis "Functions to facilitate zFPKM transformations") |
| 5147 | (description |
| 5148 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. |
| 5149 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID |
| 5150 | 24215113).") |
| 5151 | (license license:gpl3))) |
| 5152 | |
| 5153 | (define-public r-rbowtie2 |
| 5154 | (package |
| 5155 | (name "r-rbowtie2") |
| 5156 | (version "1.8.0") |
| 5157 | (source |
| 5158 | (origin |
| 5159 | (method url-fetch) |
| 5160 | (uri (bioconductor-uri "Rbowtie2" version)) |
| 5161 | (sha256 |
| 5162 | (base32 |
| 5163 | "1b7x42n9zisi2w2wwfc0c39j8s9868imyr0ysqgswf6l5mv9ivc5")))) |
| 5164 | (properties `((upstream-name . "Rbowtie2"))) |
| 5165 | (build-system r-build-system) |
| 5166 | (inputs |
| 5167 | `(("zlib" ,zlib))) |
| 5168 | (home-page "https://bioconductor.org/packages/Rbowtie2/") |
| 5169 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") |
| 5170 | (description |
| 5171 | "This package provides an R wrapper of the popular @code{bowtie2} |
| 5172 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for |
| 5173 | rapid adapter trimming, identification, and read merging.") |
| 5174 | (license license:gpl3+))) |
| 5175 | |
| 5176 | (define-public r-progeny |
| 5177 | (package |
| 5178 | (name "r-progeny") |
| 5179 | (version "1.8.0") |
| 5180 | (source |
| 5181 | (origin |
| 5182 | (method url-fetch) |
| 5183 | (uri (bioconductor-uri "progeny" version)) |
| 5184 | (sha256 |
| 5185 | (base32 |
| 5186 | "0j3kxjj7xmmwb29p87n3bw7bl38gcb94jrpw32126a578rf1pfrq")))) |
| 5187 | (build-system r-build-system) |
| 5188 | (propagated-inputs `(("r-biobase" ,r-biobase))) |
| 5189 | (home-page "https://github.com/saezlab/progeny") |
| 5190 | (synopsis "Pathway responsive gene activity inference") |
| 5191 | (description |
| 5192 | "This package provides a function to infer pathway activity from gene |
| 5193 | expression. It contains the linear model inferred in the publication |
| 5194 | \"Perturbation-response genes reveal signaling footprints in cancer gene |
| 5195 | expression\".") |
| 5196 | (license license:asl2.0))) |
| 5197 | |
| 5198 | (define-public r-arrmnormalization |
| 5199 | (package |
| 5200 | (name "r-arrmnormalization") |
| 5201 | (version "1.26.0") |
| 5202 | (source |
| 5203 | (origin |
| 5204 | (method url-fetch) |
| 5205 | (uri (bioconductor-uri "ARRmNormalization" version)) |
| 5206 | (sha256 |
| 5207 | (base32 |
| 5208 | "0jj81q454nyh4hr5c56q1hv7i4ynx3rwnvpv08w34a6m77122bi1")))) |
| 5209 | (properties |
| 5210 | `((upstream-name . "ARRmNormalization"))) |
| 5211 | (build-system r-build-system) |
| 5212 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) |
| 5213 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") |
| 5214 | (synopsis "Adaptive robust regression normalization for methylation data") |
| 5215 | (description |
| 5216 | "This is a package to perform the @dfn{Adaptive Robust Regression |
| 5217 | method} (ARRm) for the normalization of methylation data from the Illumina |
| 5218 | Infinium HumanMethylation 450k assay.") |
| 5219 | (license license:artistic2.0))) |
| 5220 | |
| 5221 | (define-public r-biocfilecache |
| 5222 | (package |
| 5223 | (name "r-biocfilecache") |
| 5224 | (version "1.10.2") |
| 5225 | (source |
| 5226 | (origin |
| 5227 | (method url-fetch) |
| 5228 | (uri (bioconductor-uri "BiocFileCache" version)) |
| 5229 | (sha256 |
| 5230 | (base32 |
| 5231 | "0jivhn95y6zv5ryamqk6nyd4l8nlskq64j362l9ml9qw746v0ja6")))) |
| 5232 | (properties `((upstream-name . "BiocFileCache"))) |
| 5233 | (build-system r-build-system) |
| 5234 | (propagated-inputs |
| 5235 | `(("r-curl" ,r-curl) |
| 5236 | ("r-dbi" ,r-dbi) |
| 5237 | ("r-dbplyr" ,r-dbplyr) |
| 5238 | ("r-dplyr" ,r-dplyr) |
| 5239 | ("r-httr" ,r-httr) |
| 5240 | ("r-rappdirs" ,r-rappdirs) |
| 5241 | ("r-rsqlite" ,r-rsqlite))) |
| 5242 | (home-page "https://bioconductor.org/packages/BiocFileCache/") |
| 5243 | (synopsis "Manage files across sessions") |
| 5244 | (description |
| 5245 | "This package creates a persistent on-disk cache of files that the user |
| 5246 | can add, update, and retrieve. It is useful for managing resources (such as |
| 5247 | custom Txdb objects) that are costly or difficult to create, web resources, |
| 5248 | and data files used across sessions.") |
| 5249 | (license license:artistic2.0))) |
| 5250 | |
| 5251 | (define-public r-iclusterplus |
| 5252 | (package |
| 5253 | (name "r-iclusterplus") |
| 5254 | (version "1.22.0") |
| 5255 | (source |
| 5256 | (origin |
| 5257 | (method url-fetch) |
| 5258 | (uri (bioconductor-uri "iClusterPlus" version)) |
| 5259 | (sha256 |
| 5260 | (base32 |
| 5261 | "1dzgfzf2x8m62hssvsn1zzag7m444kyxj2vpdxl9nk859dr5pf37")))) |
| 5262 | (properties `((upstream-name . "iClusterPlus"))) |
| 5263 | (build-system r-build-system) |
| 5264 | (native-inputs `(("gfortran" ,gfortran))) |
| 5265 | (home-page "https://bioconductor.org/packages/iClusterPlus/") |
| 5266 | (synopsis "Integrative clustering of multi-type genomic data") |
| 5267 | (description |
| 5268 | "iClusterPlus is developed for integrative clustering analysis of |
| 5269 | multi-type genomic data and is an enhanced version of iCluster proposed and |
| 5270 | developed by Shen, Olshen and Ladanyi (2009). Multi-type genomic data arise |
| 5271 | from the experiments where biological samples (e.g. tumor samples) are |
| 5272 | analyzed by multiple techniques, for instance, @dfn{array comparative genomic |
| 5273 | hybridization} (aCGH), gene expression microarray, RNA-seq and DNA-seq, and so |
| 5274 | on. In the iClusterPlus model, binary observations such as somatic mutation |
| 5275 | are modeled as Binomial processes; categorical observations such as copy |
| 5276 | number states are realizations of Multinomial random variables; counts are |
| 5277 | modeled as Poisson random processes; and continuous measures are modeled by |
| 5278 | Gaussian distributions.") |
| 5279 | (license license:gpl2+))) |
| 5280 | |
| 5281 | (define-public r-rbowtie |
| 5282 | (package |
| 5283 | (name "r-rbowtie") |
| 5284 | (version "1.26.0") |
| 5285 | (source |
| 5286 | (origin |
| 5287 | (method url-fetch) |
| 5288 | (uri (bioconductor-uri "Rbowtie" version)) |
| 5289 | (sha256 |
| 5290 | (base32 |
| 5291 | "0yy31xhdmf6xb21wlhmxxwfqpm0nil39pb2cs3pq5ia758lb88z4")))) |
| 5292 | (properties `((upstream-name . "Rbowtie"))) |
| 5293 | (build-system r-build-system) |
| 5294 | (inputs |
| 5295 | `(("zlib" ,zlib))) |
| 5296 | (home-page "https://bioconductor.org/packages/Rbowtie/") |
| 5297 | (synopsis "R bowtie wrapper") |
| 5298 | (description |
| 5299 | "This package provides an R wrapper around the popular bowtie short read |
| 5300 | aligner and around SpliceMap, a de novo splice junction discovery and |
| 5301 | alignment tool.") |
| 5302 | (license license:artistic2.0))) |
| 5303 | |
| 5304 | (define-public r-sgseq |
| 5305 | (package |
| 5306 | (name "r-sgseq") |
| 5307 | (version "1.20.0") |
| 5308 | (source |
| 5309 | (origin |
| 5310 | (method url-fetch) |
| 5311 | (uri (bioconductor-uri "SGSeq" version)) |
| 5312 | (sha256 |
| 5313 | (base32 |
| 5314 | "0950iv08wd0kjaw55rjn7m6syklvrabwr2zqq74wzyc5afyk2mrw")))) |
| 5315 | (properties `((upstream-name . "SGSeq"))) |
| 5316 | (build-system r-build-system) |
| 5317 | (propagated-inputs |
| 5318 | `(("r-annotationdbi" ,r-annotationdbi) |
| 5319 | ("r-biocgenerics" ,r-biocgenerics) |
| 5320 | ("r-biostrings" ,r-biostrings) |
| 5321 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 5322 | ("r-genomicalignments" ,r-genomicalignments) |
| 5323 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 5324 | ("r-genomicranges" ,r-genomicranges) |
| 5325 | ("r-igraph" ,r-igraph) |
| 5326 | ("r-iranges" ,r-iranges) |
| 5327 | ("r-rsamtools" ,r-rsamtools) |
| 5328 | ("r-rtracklayer" ,r-rtracklayer) |
| 5329 | ("r-runit" ,r-runit) |
| 5330 | ("r-s4vectors" ,r-s4vectors) |
| 5331 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 5332 | (home-page "https://bioconductor.org/packages/SGSeq/") |
| 5333 | (synopsis "Splice event prediction and quantification from RNA-seq data") |
| 5334 | (description |
| 5335 | "SGSeq is a package for analyzing splice events from RNA-seq data. Input |
| 5336 | data are RNA-seq reads mapped to a reference genome in BAM format. Genes are |
| 5337 | represented as a splice graph, which can be obtained from existing annotation |
| 5338 | or predicted from the mapped sequence reads. Splice events are identified |
| 5339 | from the graph and are quantified locally using structurally compatible reads |
| 5340 | at the start or end of each splice variant. The software includes functions |
| 5341 | for splice event prediction, quantification, visualization and |
| 5342 | interpretation.") |
| 5343 | (license license:artistic2.0))) |
| 5344 | |
| 5345 | (define-public r-rhisat2 |
| 5346 | (package |
| 5347 | (name "r-rhisat2") |
| 5348 | (version "1.2.0") |
| 5349 | (source |
| 5350 | (origin |
| 5351 | (method url-fetch) |
| 5352 | (uri (bioconductor-uri "Rhisat2" version)) |
| 5353 | (sha256 |
| 5354 | (base32 |
| 5355 | "02fn5cm8sj2s9x00505y3iyipn1r3lpvpwpjy2pdxdbpmhb5hy49")))) |
| 5356 | (properties `((upstream-name . "Rhisat2"))) |
| 5357 | (build-system r-build-system) |
| 5358 | (arguments |
| 5359 | `(#:phases |
| 5360 | (modify-phases %standard-phases |
| 5361 | (add-after 'unpack 'make-reproducible |
| 5362 | (lambda _ |
| 5363 | (substitute* "src/Makefile" |
| 5364 | (("`hostname`") "guix") |
| 5365 | (("`date`") "0") |
| 5366 | ;; Avoid shelling out to "which". |
| 5367 | (("^CC =.*") (which "gcc")) |
| 5368 | (("^CPP =.*") (which "g++"))) |
| 5369 | #t))))) |
| 5370 | (propagated-inputs |
| 5371 | `(("r-genomicfeatures" ,r-genomicfeatures) |
| 5372 | ("r-genomicranges" ,r-genomicranges) |
| 5373 | ("r-sgseq" ,r-sgseq))) |
| 5374 | (home-page "https://github.com/fmicompbio/Rhisat2") |
| 5375 | (synopsis "R Wrapper for HISAT2 sequence aligner") |
| 5376 | (description |
| 5377 | "This package provides an R interface to the HISAT2 spliced short-read |
| 5378 | aligner by Kim et al. (2015). The package contains wrapper functions to |
| 5379 | create a genome index and to perform the read alignment to the generated |
| 5380 | index.") |
| 5381 | (license license:gpl3))) |
| 5382 | |
| 5383 | (define-public r-quasr |
| 5384 | (package |
| 5385 | (name "r-quasr") |
| 5386 | (version "1.26.0") |
| 5387 | (source |
| 5388 | (origin |
| 5389 | (method url-fetch) |
| 5390 | (uri (bioconductor-uri "QuasR" version)) |
| 5391 | (sha256 |
| 5392 | (base32 |
| 5393 | "07m5q7wasapj2984kwy897510flbhvz7x0fgs7q2vm5wjhfzdrgv")))) |
| 5394 | (properties `((upstream-name . "QuasR"))) |
| 5395 | (build-system r-build-system) |
| 5396 | (inputs |
| 5397 | `(("zlib" ,zlib))) |
| 5398 | (propagated-inputs |
| 5399 | `(("r-annotationdbi" ,r-annotationdbi) |
| 5400 | ("r-biobase" ,r-biobase) |
| 5401 | ("r-biocgenerics" ,r-biocgenerics) |
| 5402 | ("r-biocmanager" ,r-biocmanager) |
| 5403 | ("r-biocparallel" ,r-biocparallel) |
| 5404 | ("r-biostrings" ,r-biostrings) |
| 5405 | ("r-bsgenome" ,r-bsgenome) |
| 5406 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 5407 | ("r-genomicalignments" ,r-genomicalignments) |
| 5408 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 5409 | ("r-genomicfiles" ,r-genomicfiles) |
| 5410 | ("r-genomicranges" ,r-genomicranges) |
| 5411 | ("r-iranges" ,r-iranges) |
| 5412 | ("r-rbowtie" ,r-rbowtie) |
| 5413 | ("r-rhisat2" ,r-rhisat2) |
| 5414 | ("r-rhtslib" ,r-rhtslib) |
| 5415 | ("r-rsamtools" ,r-rsamtools) |
| 5416 | ("r-rtracklayer" ,r-rtracklayer) |
| 5417 | ("r-s4vectors" ,r-s4vectors) |
| 5418 | ("r-shortread" ,r-shortread))) |
| 5419 | (home-page "https://bioconductor.org/packages/QuasR/") |
| 5420 | (synopsis "Quantify and annotate short reads in R") |
| 5421 | (description |
| 5422 | "This package provides a framework for the quantification and analysis of |
| 5423 | short genomic reads. It covers a complete workflow starting from raw sequence |
| 5424 | reads, over creation of alignments and quality control plots, to the |
| 5425 | quantification of genomic regions of interest.") |
| 5426 | (license license:gpl2))) |
| 5427 | |
| 5428 | (define-public r-rqc |
| 5429 | (package |
| 5430 | (name "r-rqc") |
| 5431 | (version "1.20.0") |
| 5432 | (source |
| 5433 | (origin |
| 5434 | (method url-fetch) |
| 5435 | (uri (bioconductor-uri "Rqc" version)) |
| 5436 | (sha256 |
| 5437 | (base32 |
| 5438 | "1nxkrb9kx41g050yz935yrl9pjkakhr8v6whxcvr72gg4r9m2x3m")))) |
| 5439 | (properties `((upstream-name . "Rqc"))) |
| 5440 | (build-system r-build-system) |
| 5441 | (propagated-inputs |
| 5442 | `(("r-biocgenerics" ,r-biocgenerics) |
| 5443 | ("r-biocparallel" ,r-biocparallel) |
| 5444 | ("r-biocstyle" ,r-biocstyle) |
| 5445 | ("r-biostrings" ,r-biostrings) |
| 5446 | ("r-biovizbase" ,r-biovizbase) |
| 5447 | ("r-genomicalignments" ,r-genomicalignments) |
| 5448 | ("r-genomicfiles" ,r-genomicfiles) |
| 5449 | ("r-ggplot2" ,r-ggplot2) |
| 5450 | ("r-iranges" ,r-iranges) |
| 5451 | ("r-knitr" ,r-knitr) |
| 5452 | ("r-markdown" ,r-markdown) |
| 5453 | ("r-plyr" ,r-plyr) |
| 5454 | ("r-rcpp" ,r-rcpp) |
| 5455 | ("r-reshape2" ,r-reshape2) |
| 5456 | ("r-rsamtools" ,r-rsamtools) |
| 5457 | ("r-s4vectors" ,r-s4vectors) |
| 5458 | ("r-shiny" ,r-shiny) |
| 5459 | ("r-shortread" ,r-shortread))) |
| 5460 | (home-page "https://github.com/labbcb/Rqc") |
| 5461 | (synopsis "Quality control tool for high-throughput sequencing data") |
| 5462 | (description |
| 5463 | "Rqc is an optimized tool designed for quality control and assessment of |
| 5464 | high-throughput sequencing data. It performs parallel processing of entire |
| 5465 | files and produces a report which contains a set of high-resolution |
| 5466 | graphics.") |
| 5467 | (license license:gpl2+))) |
| 5468 | |
| 5469 | (define-public r-birewire |
| 5470 | (package |
| 5471 | (name "r-birewire") |
| 5472 | (version "3.18.0") |
| 5473 | (source |
| 5474 | (origin |
| 5475 | (method url-fetch) |
| 5476 | (uri (bioconductor-uri "BiRewire" version)) |
| 5477 | (sha256 |
| 5478 | (base32 |
| 5479 | "1074cp422ail72yajn8p0bg26h6zzz07nzypnwfyv86qrpvpdw9q")))) |
| 5480 | (properties `((upstream-name . "BiRewire"))) |
| 5481 | (build-system r-build-system) |
| 5482 | (propagated-inputs |
| 5483 | `(("r-igraph" ,r-igraph) |
| 5484 | ("r-matrix" ,r-matrix) |
| 5485 | ("r-slam" ,r-slam) |
| 5486 | ("r-tsne" ,r-tsne))) |
| 5487 | (home-page "https://bioconductor.org/packages/release/bioc/html/BiRewire.html") |
| 5488 | (synopsis "Tools for randomization of bipartite graphs") |
| 5489 | (description |
| 5490 | "This package provides functions for bipartite network rewiring through N |
| 5491 | consecutive switching steps and for the computation of the minimal number of |
| 5492 | switching steps to be performed in order to maximise the dissimilarity with |
| 5493 | respect to the original network. It includes functions for the analysis of |
| 5494 | the introduced randomness across the switching steps and several other |
| 5495 | routines to analyse the resulting networks and their natural projections.") |
| 5496 | (license license:gpl3))) |
| 5497 | |
| 5498 | (define-public r-birta |
| 5499 | (package |
| 5500 | (name "r-birta") |
| 5501 | (version "1.30.0") |
| 5502 | (source |
| 5503 | (origin |
| 5504 | (method url-fetch) |
| 5505 | (uri (bioconductor-uri "birta" version)) |
| 5506 | (sha256 |
| 5507 | (base32 |
| 5508 | "1zhlwapdgkz0fpv5bqfxh9aw6ymnmxnnm1r0n0kfzn5izyjavslg")))) |
| 5509 | (build-system r-build-system) |
| 5510 | (propagated-inputs |
| 5511 | `(("r-biobase" ,r-biobase) |
| 5512 | ("r-limma" ,r-limma) |
| 5513 | ("r-mass" ,r-mass))) |
| 5514 | (home-page "https://bioconductor.org/packages/birta") |
| 5515 | (synopsis "Bayesian inference of regulation of transcriptional activity") |
| 5516 | (description |
| 5517 | "Expression levels of mRNA molecules are regulated by different |
| 5518 | processes, comprising inhibition or activation by transcription factors and |
| 5519 | post-transcriptional degradation by microRNAs. @dfn{birta} (Bayesian |
| 5520 | Inference of Regulation of Transcriptional Activity) uses the regulatory |
| 5521 | networks of transcription factors and miRNAs together with mRNA and miRNA |
| 5522 | expression data to predict switches in regulatory activity between two |
| 5523 | conditions. A Bayesian network is used to model the regulatory structure and |
| 5524 | Markov-Chain-Monte-Carlo is applied to sample the activity states.") |
| 5525 | (license license:gpl2+))) |
| 5526 | |
| 5527 | (define-public r-multidataset |
| 5528 | (package |
| 5529 | (name "r-multidataset") |
| 5530 | (version "1.14.0") |
| 5531 | (source |
| 5532 | (origin |
| 5533 | (method url-fetch) |
| 5534 | (uri (bioconductor-uri "MultiDataSet" version)) |
| 5535 | (sha256 |
| 5536 | (base32 |
| 5537 | "0iw99ymrv3ls023mpmgyagmb5simgsgadpj0k4bnssfaqnklywlj")))) |
| 5538 | (properties `((upstream-name . "MultiDataSet"))) |
| 5539 | (build-system r-build-system) |
| 5540 | (propagated-inputs |
| 5541 | `(("r-biobase" ,r-biobase) |
| 5542 | ("r-biocgenerics" ,r-biocgenerics) |
| 5543 | ("r-genomicranges" ,r-genomicranges) |
| 5544 | ("r-ggplot2" ,r-ggplot2) |
| 5545 | ("r-ggrepel" ,r-ggrepel) |
| 5546 | ("r-iranges" ,r-iranges) |
| 5547 | ("r-limma" ,r-limma) |
| 5548 | ("r-qqman" ,r-qqman) |
| 5549 | ("r-s4vectors" ,r-s4vectors) |
| 5550 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 5551 | (home-page "https://bioconductor.org/packages/MultiDataSet/") |
| 5552 | (synopsis "Implementation of MultiDataSet and ResultSet") |
| 5553 | (description |
| 5554 | "This package provides an implementation of the BRGE's (Bioinformatic |
| 5555 | Research Group in Epidemiology from Center for Research in Environmental |
| 5556 | Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for |
| 5557 | integrating multi omics data sets and ResultSet is a container for omics |
| 5558 | results. This package contains base classes for MEAL and rexposome |
| 5559 | packages.") |
| 5560 | (license license:expat))) |
| 5561 | |
| 5562 | (define-public r-ropls |
| 5563 | (package |
| 5564 | (name "r-ropls") |
| 5565 | (version "1.18.8") |
| 5566 | (source |
| 5567 | (origin |
| 5568 | (method url-fetch) |
| 5569 | (uri (bioconductor-uri "ropls" version)) |
| 5570 | (sha256 |
| 5571 | (base32 |
| 5572 | "033i39r4037nd54jnp5zdn1vpzh61r671vmq0sf8dqrfblhm4w7a")))) |
| 5573 | (build-system r-build-system) |
| 5574 | (propagated-inputs |
| 5575 | `(("r-biobase" ,r-biobase) |
| 5576 | ("r-multidataset" ,r-multidataset))) |
| 5577 | (native-inputs |
| 5578 | `(("r-knitr" ,r-knitr))) ; for vignettes |
| 5579 | (home-page "https://dx.doi.org/10.1021/acs.jproteome.5b00354") |
| 5580 | (synopsis "Multivariate analysis and feature selection of omics data") |
| 5581 | (description |
| 5582 | "Latent variable modeling with @dfn{Principal Component Analysis} (PCA) |
| 5583 | and @dfn{Partial Least Squares} (PLS) are powerful methods for visualization, |
| 5584 | regression, classification, and feature selection of omics data where the |
| 5585 | number of variables exceeds the number of samples and with multicollinearity |
| 5586 | among variables. @dfn{Orthogonal Partial Least Squares} (OPLS) enables to |
| 5587 | separately model the variation correlated (predictive) to the factor of |
| 5588 | interest and the uncorrelated (orthogonal) variation. While performing |
| 5589 | similarly to PLS, OPLS facilitates interpretation. |
| 5590 | |
| 5591 | This package provides imlementations of PCA, PLS, and OPLS for multivariate |
| 5592 | analysis and feature selection of omics data. In addition to scores, loadings |
| 5593 | and weights plots, the package provides metrics and graphics to determine the |
| 5594 | optimal number of components (e.g. with the R2 and Q2 coefficients), check the |
| 5595 | validity of the model by permutation testing, detect outliers, and perform |
| 5596 | feature selection (e.g. with Variable Importance in Projection or regression |
| 5597 | coefficients).") |
| 5598 | (license license:cecill))) |
| 5599 | |
| 5600 | (define-public r-biosigner |
| 5601 | (package |
| 5602 | (name "r-biosigner") |
| 5603 | (version "1.14.4") |
| 5604 | (source |
| 5605 | (origin |
| 5606 | (method url-fetch) |
| 5607 | (uri (bioconductor-uri "biosigner" version)) |
| 5608 | (sha256 |
| 5609 | (base32 |
| 5610 | "0hypk784xcax99mp673md6kvx45chk2nxbqniww7zm9q2hj983hl")))) |
| 5611 | (build-system r-build-system) |
| 5612 | (propagated-inputs |
| 5613 | `(("r-biobase" ,r-biobase) |
| 5614 | ("r-e1071" ,r-e1071) |
| 5615 | ("r-multidataset" ,r-multidataset) |
| 5616 | ("r-randomforest" ,r-randomforest) |
| 5617 | ("r-ropls" ,r-ropls))) |
| 5618 | (native-inputs |
| 5619 | `(("r-knitr" ,r-knitr))) |
| 5620 | (home-page "https://bioconductor.org/packages/biosigner/") |
| 5621 | (synopsis "Signature discovery from omics data") |
| 5622 | (description |
| 5623 | "Feature selection is critical in omics data analysis to extract |
| 5624 | restricted and meaningful molecular signatures from complex and high-dimension |
| 5625 | data, and to build robust classifiers. This package implements a method to |
| 5626 | assess the relevance of the variables for the prediction performances of the |
| 5627 | classifier. The approach can be run in parallel with the PLS-DA, Random |
| 5628 | Forest, and SVM binary classifiers. The signatures and the corresponding |
| 5629 | 'restricted' models are returned, enabling future predictions on new |
| 5630 | datasets.") |
| 5631 | (license license:cecill))) |
| 5632 | |
| 5633 | (define-public r-annotatr |
| 5634 | (package |
| 5635 | (name "r-annotatr") |
| 5636 | (version "1.12.1") |
| 5637 | (source |
| 5638 | (origin |
| 5639 | (method url-fetch) |
| 5640 | (uri (bioconductor-uri "annotatr" version)) |
| 5641 | (sha256 |
| 5642 | (base32 |
| 5643 | "1bibk3p1q4cavqy11xs6rqqhqdjsq2dd7lf7blwcr27s5ajcd6dj")))) |
| 5644 | (build-system r-build-system) |
| 5645 | (propagated-inputs |
| 5646 | `(("r-annotationdbi" ,r-annotationdbi) |
| 5647 | ("r-annotationhub" ,r-annotationhub) |
| 5648 | ("r-dplyr" ,r-dplyr) |
| 5649 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 5650 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 5651 | ("r-genomicranges" ,r-genomicranges) |
| 5652 | ("r-ggplot2" ,r-ggplot2) |
| 5653 | ("r-iranges" ,r-iranges) |
| 5654 | ("r-readr" ,r-readr) |
| 5655 | ("r-regioner" ,r-regioner) |
| 5656 | ("r-reshape2" ,r-reshape2) |
| 5657 | ("r-rtracklayer" ,r-rtracklayer) |
| 5658 | ("r-s4vectors" ,r-s4vectors))) |
| 5659 | (home-page "https://bioconductor.org/packages/annotatr/") |
| 5660 | (synopsis "Annotation of genomic regions to genomic annotations") |
| 5661 | (description |
| 5662 | "Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, |
| 5663 | differentially methylated CpGs or regions, SNPs, etc.) it is often of interest |
| 5664 | to investigate the intersecting genomic annotations. Such annotations include |
| 5665 | those relating to gene models (promoters, 5'UTRs, exons, introns, and 3'UTRs), |
| 5666 | CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as |
| 5667 | enhancers. The annotatr package provides an easy way to summarize and |
| 5668 | visualize the intersection of genomic sites/regions with genomic |
| 5669 | annotations.") |
| 5670 | (license license:gpl3))) |
| 5671 | |
| 5672 | (define-public r-rsubread |
| 5673 | (package |
| 5674 | (name "r-rsubread") |
| 5675 | (version "2.0.1") |
| 5676 | (source |
| 5677 | (origin |
| 5678 | (method url-fetch) |
| 5679 | (uri (bioconductor-uri "Rsubread" version)) |
| 5680 | (sha256 |
| 5681 | (base32 |
| 5682 | "0pdkx9mhvzw3a4ff725qvda9bxvs9vh2ppb29cc5jrivgjndv5cy")))) |
| 5683 | (properties `((upstream-name . "Rsubread"))) |
| 5684 | (build-system r-build-system) |
| 5685 | (inputs `(("zlib" ,zlib))) |
| 5686 | (home-page "https://bioconductor.org/packages/Rsubread/") |
| 5687 | (synopsis "Subread sequence alignment and counting for R") |
| 5688 | (description |
| 5689 | "This package provides tools for alignment, quantification and analysis |
| 5690 | of second and third generation sequencing data. It includes functionality for |
| 5691 | read mapping, read counting, SNP calling, structural variant detection and |
| 5692 | gene fusion discovery. It can be applied to all major sequencing techologies |
| 5693 | and to both short and long sequence reads.") |
| 5694 | (license license:gpl3))) |
| 5695 | |
| 5696 | (define-public r-flowutils |
| 5697 | (package |
| 5698 | (name "r-flowutils") |
| 5699 | (version "1.50.0") |
| 5700 | (source |
| 5701 | (origin |
| 5702 | (method url-fetch) |
| 5703 | (uri (bioconductor-uri "flowUtils" version)) |
| 5704 | (sha256 |
| 5705 | (base32 |
| 5706 | "1xcs19j9p3izvksyy5wzsbicwby0dsa9g2w7gjzwynzgj5dpfr81")))) |
| 5707 | (properties `((upstream-name . "flowUtils"))) |
| 5708 | (build-system r-build-system) |
| 5709 | (propagated-inputs |
| 5710 | `(("r-biobase" ,r-biobase) |
| 5711 | ("r-corpcor" ,r-corpcor) |
| 5712 | ("r-flowcore" ,r-flowcore) |
| 5713 | ("r-graph" ,r-graph) |
| 5714 | ("r-runit" ,r-runit) |
| 5715 | ("r-xml" ,r-xml))) |
| 5716 | (home-page "https://github.com/jspidlen/flowUtils") |
| 5717 | (synopsis "Utilities for flow cytometry") |
| 5718 | (description |
| 5719 | "This package provides utilities for flow cytometry data.") |
| 5720 | (license license:artistic2.0))) |
| 5721 | |
| 5722 | (define-public r-consensusclusterplus |
| 5723 | (package |
| 5724 | (name "r-consensusclusterplus") |
| 5725 | (version "1.50.0") |
| 5726 | (source |
| 5727 | (origin |
| 5728 | (method url-fetch) |
| 5729 | (uri (bioconductor-uri "ConsensusClusterPlus" version)) |
| 5730 | (sha256 |
| 5731 | (base32 |
| 5732 | "0pnh5zy6d3c364xxjdn5zp3kf5afhsxv6yzkdn1qspny0pmqlrp4")))) |
| 5733 | (properties |
| 5734 | `((upstream-name . "ConsensusClusterPlus"))) |
| 5735 | (build-system r-build-system) |
| 5736 | (propagated-inputs |
| 5737 | `(("r-all" ,r-all) |
| 5738 | ("r-biobase" ,r-biobase) |
| 5739 | ("r-cluster" ,r-cluster))) |
| 5740 | (home-page "https://bioconductor.org/packages/ConsensusClusterPlus") |
| 5741 | (synopsis "Clustering algorithm") |
| 5742 | (description |
| 5743 | "This package provides an implementation of an algorithm for determining |
| 5744 | cluster count and membership by stability evidence in unsupervised analysis.") |
| 5745 | (license license:gpl2))) |
| 5746 | |
| 5747 | (define-public r-cytolib |
| 5748 | (package |
| 5749 | (name "r-cytolib") |
| 5750 | (version "1.8.0") |
| 5751 | (source |
| 5752 | (origin |
| 5753 | (method url-fetch) |
| 5754 | (uri (bioconductor-uri "cytolib" version)) |
| 5755 | (sha256 |
| 5756 | (base32 |
| 5757 | "1zk5i09k782lw6297gl3rh0g4fxswr2ang8dgqj7p0814l7h15k9")))) |
| 5758 | (properties `((upstream-name . "cytolib"))) |
| 5759 | (build-system r-build-system) |
| 5760 | (home-page "https://bioconductor.org/packages/cytolib/") |
| 5761 | (synopsis "C++ infrastructure for working with gated cytometry") |
| 5762 | (description |
| 5763 | "This package provides the core data structure and API to represent and |
| 5764 | interact with gated cytometry data.") |
| 5765 | (license license:artistic2.0))) |
| 5766 | |
| 5767 | (define-public r-flowcore |
| 5768 | (package |
| 5769 | (name "r-flowcore") |
| 5770 | (version "1.52.1") |
| 5771 | (source |
| 5772 | (origin |
| 5773 | (method url-fetch) |
| 5774 | (uri (bioconductor-uri "flowCore" version)) |
| 5775 | (sha256 |
| 5776 | (base32 |
| 5777 | "08kvxc187iwlixibx1860jcp5g9bsw8abkv06x2qv1w83fas4pp2")))) |
| 5778 | (properties `((upstream-name . "flowCore"))) |
| 5779 | (build-system r-build-system) |
| 5780 | (propagated-inputs |
| 5781 | `(("r-bh" ,r-bh) |
| 5782 | ("r-biobase" ,r-biobase) |
| 5783 | ("r-biocgenerics" ,r-biocgenerics) |
| 5784 | ("r-cytolib" ,r-cytolib) |
| 5785 | ("r-matrixstats" ,r-matrixstats) |
| 5786 | ("r-rcpp" ,r-rcpp))) |
| 5787 | (home-page "https://bioconductor.org/packages/flowCore") |
| 5788 | (synopsis "Basic structures for flow cytometry data") |
| 5789 | (description |
| 5790 | "This package provides S4 data structures and basic functions to deal |
| 5791 | with flow cytometry data.") |
| 5792 | (license license:artistic2.0))) |
| 5793 | |
| 5794 | (define-public r-flowmeans |
| 5795 | (package |
| 5796 | (name "r-flowmeans") |
| 5797 | (version "1.46.0") |
| 5798 | (source |
| 5799 | (origin |
| 5800 | (method url-fetch) |
| 5801 | (uri (bioconductor-uri "flowMeans" version)) |
| 5802 | (sha256 |
| 5803 | (base32 |
| 5804 | "1yisrikaafmpb4sig2c5l0wcz4idrs4as7i9x90v6z2v94iq0m8h")))) |
| 5805 | (properties `((upstream-name . "flowMeans"))) |
| 5806 | (build-system r-build-system) |
| 5807 | (propagated-inputs |
| 5808 | `(("r-biobase" ,r-biobase) |
| 5809 | ("r-feature" ,r-feature) |
| 5810 | ("r-flowcore" ,r-flowcore) |
| 5811 | ("r-rrcov" ,r-rrcov))) |
| 5812 | (home-page "https://bioconductor.org/packages/flowMeans") |
| 5813 | (synopsis "Non-parametric flow cytometry data gating") |
| 5814 | (description |
| 5815 | "This package provides tools to identify cell populations in Flow |
| 5816 | Cytometry data using non-parametric clustering and segmented-regression-based |
| 5817 | change point detection.") |
| 5818 | (license license:artistic2.0))) |
| 5819 | |
| 5820 | (define-public r-ncdfflow |
| 5821 | (package |
| 5822 | (name "r-ncdfflow") |
| 5823 | (version "2.32.0") |
| 5824 | (source |
| 5825 | (origin |
| 5826 | (method url-fetch) |
| 5827 | (uri (bioconductor-uri "ncdfFlow" version)) |
| 5828 | (sha256 |
| 5829 | (base32 |
| 5830 | "06lscx6h4rg80ifi90rj7z2497b8w1fjipm3l8s3230rkizhh02i")))) |
| 5831 | (properties `((upstream-name . "ncdfFlow"))) |
| 5832 | (build-system r-build-system) |
| 5833 | (inputs |
| 5834 | `(("zlib" ,zlib))) |
| 5835 | (propagated-inputs |
| 5836 | `(("r-bh" ,r-bh) |
| 5837 | ("r-biobase" ,r-biobase) |
| 5838 | ("r-biocgenerics" ,r-biocgenerics) |
| 5839 | ("r-flowcore" ,r-flowcore) |
| 5840 | ("r-rcpp" ,r-rcpp) |
| 5841 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
| 5842 | ("r-rhdf5lib" ,r-rhdf5lib) |
| 5843 | ("r-zlibbioc" ,r-zlibbioc))) |
| 5844 | (home-page "https://bioconductor.org/packages/ncdfFlow/") |
| 5845 | (synopsis "HDF5 based storage for flow cytometry data") |
| 5846 | (description |
| 5847 | "This package provides HDF5 storage based methods and functions for |
| 5848 | manipulation of flow cytometry data.") |
| 5849 | (license license:artistic2.0))) |
| 5850 | |
| 5851 | (define-public r-ggcyto |
| 5852 | (package |
| 5853 | (name "r-ggcyto") |
| 5854 | (version "1.14.1") |
| 5855 | (source |
| 5856 | (origin |
| 5857 | (method url-fetch) |
| 5858 | (uri (bioconductor-uri "ggcyto" version)) |
| 5859 | (sha256 |
| 5860 | (base32 |
| 5861 | "16jwdslhmj1nsa28wmaircy15cq7qn8nsyiawinjv711qiqhgw50")))) |
| 5862 | (properties `((upstream-name . "ggcyto"))) |
| 5863 | (build-system r-build-system) |
| 5864 | (propagated-inputs |
| 5865 | `(("r-data-table" ,r-data-table) |
| 5866 | ("r-flowcore" ,r-flowcore) |
| 5867 | ("r-flowworkspace" ,r-flowworkspace) |
| 5868 | ("r-ggplot2" ,r-ggplot2) |
| 5869 | ("r-gridextra" ,r-gridextra) |
| 5870 | ("r-ncdfflow" ,r-ncdfflow) |
| 5871 | ("r-plyr" ,r-plyr) |
| 5872 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 5873 | ("r-rlang" ,r-rlang) |
| 5874 | ("r-scales" ,r-scales))) |
| 5875 | (native-inputs |
| 5876 | `(("r-knitr" ,r-knitr))) |
| 5877 | (home-page "https://github.com/RGLab/ggcyto/issues") |
| 5878 | (synopsis "Visualize Cytometry data with ggplot") |
| 5879 | (description |
| 5880 | "With the dedicated fortify method implemented for @code{flowSet}, |
| 5881 | @code{ncdfFlowSet} and @code{GatingSet} classes, both raw and gated flow |
| 5882 | cytometry data can be plotted directly with ggplot. The @code{ggcyto} wrapper |
| 5883 | and some custom layers also make it easy to add gates and population |
| 5884 | statistics to the plot.") |
| 5885 | (license license:artistic2.0))) |
| 5886 | |
| 5887 | (define-public r-flowviz |
| 5888 | (package |
| 5889 | (name "r-flowviz") |
| 5890 | (version "1.50.0") |
| 5891 | (source |
| 5892 | (origin |
| 5893 | (method url-fetch) |
| 5894 | (uri (bioconductor-uri "flowViz" version)) |
| 5895 | (sha256 |
| 5896 | (base32 |
| 5897 | "0ik16bxcfcg3q26ra3055718kskid64aaazcbqsxalca9ppdm4k7")))) |
| 5898 | (properties `((upstream-name . "flowViz"))) |
| 5899 | (build-system r-build-system) |
| 5900 | (propagated-inputs |
| 5901 | `(("r-biobase" ,r-biobase) |
| 5902 | ("r-flowcore" ,r-flowcore) |
| 5903 | ("r-hexbin" ,r-hexbin) |
| 5904 | ("r-idpmisc" ,r-idpmisc) |
| 5905 | ("r-kernsmooth" ,r-kernsmooth) |
| 5906 | ("r-lattice" ,r-lattice) |
| 5907 | ("r-latticeextra" ,r-latticeextra) |
| 5908 | ("r-mass" ,r-mass) |
| 5909 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 5910 | (home-page "https://bioconductor.org/packages/flowViz/") |
| 5911 | (synopsis "Visualization for flow cytometry") |
| 5912 | (description |
| 5913 | "This package provides visualization tools for flow cytometry data.") |
| 5914 | (license license:artistic2.0))) |
| 5915 | |
| 5916 | (define-public r-flowclust |
| 5917 | (package |
| 5918 | (name "r-flowclust") |
| 5919 | (version "3.24.0") |
| 5920 | (source |
| 5921 | (origin |
| 5922 | (method url-fetch) |
| 5923 | (uri (bioconductor-uri "flowClust" version)) |
| 5924 | (sha256 |
| 5925 | (base32 |
| 5926 | "0k4bgc4mf512njfdfg5ld9l7slgfxyfh766jab87j96zrrgcnj8s")))) |
| 5927 | (properties `((upstream-name . "flowClust"))) |
| 5928 | (build-system r-build-system) |
| 5929 | (arguments |
| 5930 | `(#:configure-flags |
| 5931 | (list "--configure-args=--enable-bundled-gsl=no"))) |
| 5932 | (propagated-inputs |
| 5933 | `(("r-biobase" ,r-biobase) |
| 5934 | ("r-biocgenerics" ,r-biocgenerics) |
| 5935 | ("r-clue" ,r-clue) |
| 5936 | ("r-corpcor" ,r-corpcor) |
| 5937 | ("r-ellipse" ,r-ellipse) |
| 5938 | ("r-flowcore" ,r-flowcore) |
| 5939 | ("r-flowviz" ,r-flowviz) |
| 5940 | ("r-graph" ,r-graph) |
| 5941 | ("r-mnormt" ,r-mnormt))) |
| 5942 | (inputs |
| 5943 | `(("gsl" ,gsl))) |
| 5944 | (native-inputs |
| 5945 | `(("pkg-config" ,pkg-config))) |
| 5946 | (home-page "https://bioconductor.org/packages/flowClust") |
| 5947 | (synopsis "Clustering for flow cytometry") |
| 5948 | (description |
| 5949 | "This package provides robust model-based clustering using a t-mixture |
| 5950 | model with Box-Cox transformation.") |
| 5951 | (license license:artistic2.0))) |
| 5952 | |
| 5953 | ;; TODO: this package bundles an old version of protobuf. It's not easy to |
| 5954 | ;; make it use our protobuf package instead. |
| 5955 | (define-public r-rprotobuflib |
| 5956 | (package |
| 5957 | (name "r-rprotobuflib") |
| 5958 | (version "1.8.0") |
| 5959 | (source |
| 5960 | (origin |
| 5961 | (method url-fetch) |
| 5962 | (uri (bioconductor-uri "RProtoBufLib" version)) |
| 5963 | (sha256 |
| 5964 | (base32 |
| 5965 | "0dlgki21a37bxqh3cf83vl5zqxm86472g8a9plvhrjzzsn3mwnrm")))) |
| 5966 | (properties `((upstream-name . "RProtoBufLib"))) |
| 5967 | (build-system r-build-system) |
| 5968 | (arguments |
| 5969 | `(#:phases |
| 5970 | (modify-phases %standard-phases |
| 5971 | (add-after 'unpack 'unpack-bundled-sources |
| 5972 | (lambda _ |
| 5973 | (with-directory-excursion "src" |
| 5974 | (invoke "tar" "xf" "protobuf-2.6.0.tgz")) |
| 5975 | #t))))) |
| 5976 | (home-page "https://bioconductor.org/packages/RProtoBufLib/") |
| 5977 | (synopsis "C++ headers and static libraries of Protocol buffers") |
| 5978 | (description |
| 5979 | "This package provides the headers and static library of Protocol buffers |
| 5980 | for other R packages to compile and link against.") |
| 5981 | (license license:bsd-3))) |
| 5982 | |
| 5983 | (define-public r-flowworkspace |
| 5984 | (package |
| 5985 | (name "r-flowworkspace") |
| 5986 | (version "3.34.1") |
| 5987 | (source |
| 5988 | (origin |
| 5989 | (method url-fetch) |
| 5990 | (uri (bioconductor-uri "flowWorkspace" version)) |
| 5991 | (sha256 |
| 5992 | (base32 |
| 5993 | "1ijbc6z9ljhrw3cqr02smgplhrfg44gzrb1dq4gbrpq3nj4khhpn")))) |
| 5994 | (properties `((upstream-name . "flowWorkspace"))) |
| 5995 | (build-system r-build-system) |
| 5996 | (propagated-inputs |
| 5997 | `(("r-bh" ,r-bh) |
| 5998 | ("r-biobase" ,r-biobase) |
| 5999 | ("r-biocgenerics" ,r-biocgenerics) |
| 6000 | ("r-cytolib" ,r-cytolib) |
| 6001 | ("r-data-table" ,r-data-table) |
| 6002 | ("r-digest" ,r-digest) |
| 6003 | ("r-dplyr" ,r-dplyr) |
| 6004 | ("r-flowcore" ,r-flowcore) |
| 6005 | ("r-flowviz" ,r-flowviz) |
| 6006 | ("r-graph" ,r-graph) |
| 6007 | ("r-gridextra" ,r-gridextra) |
| 6008 | ("r-lattice" ,r-lattice) |
| 6009 | ("r-latticeextra" ,r-latticeextra) |
| 6010 | ("r-matrixstats" ,r-matrixstats) |
| 6011 | ("r-ncdfflow" ,r-ncdfflow) |
| 6012 | ("r-rbgl" ,r-rbgl) |
| 6013 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 6014 | ("r-rcpp" ,r-rcpp) |
| 6015 | ("r-rcppparallel" ,r-rcppparallel) |
| 6016 | ("r-rgraphviz" ,r-rgraphviz) |
| 6017 | ("r-rprotobuflib" ,r-rprotobuflib) |
| 6018 | ("r-scales" ,r-scales) |
| 6019 | ("r-stringr" ,r-stringr))) |
| 6020 | (home-page "https://bioconductor.org/packages/flowWorkspace/") |
| 6021 | (synopsis "Infrastructure for working with cytometry data") |
| 6022 | (description |
| 6023 | "This package is designed to facilitate comparison of automated gating |
| 6024 | methods against manual gating done in flowJo. This package allows you to |
| 6025 | import basic flowJo workspaces into BioConductor and replicate the gating from |
| 6026 | flowJo using the @code{flowCore} functionality. Gating hierarchies, groups of |
| 6027 | samples, compensation, and transformation are performed so that the output |
| 6028 | matches the flowJo analysis.") |
| 6029 | (license license:artistic2.0))) |
| 6030 | |
| 6031 | (define-public r-flowstats |
| 6032 | (package |
| 6033 | (name "r-flowstats") |
| 6034 | (version "3.44.0") |
| 6035 | (source |
| 6036 | (origin |
| 6037 | (method url-fetch) |
| 6038 | (uri (bioconductor-uri "flowStats" version)) |
| 6039 | (sha256 |
| 6040 | (base32 |
| 6041 | "0pql0lpf90nra7w6z6nd8l9cgjlsg2pxysfravnbzfhl3pjvd96w")))) |
| 6042 | (properties `((upstream-name . "flowStats"))) |
| 6043 | (build-system r-build-system) |
| 6044 | (propagated-inputs |
| 6045 | `(("r-biobase" ,r-biobase) |
| 6046 | ("r-biocgenerics" ,r-biocgenerics) |
| 6047 | ("r-cluster" ,r-cluster) |
| 6048 | ("r-fda" ,r-fda) |
| 6049 | ("r-flowcore" ,r-flowcore) |
| 6050 | ("r-flowviz" ,r-flowviz) |
| 6051 | ("r-flowworkspace" ,r-flowworkspace) |
| 6052 | ("r-kernsmooth" ,r-kernsmooth) |
| 6053 | ("r-ks" ,r-ks) |
| 6054 | ("r-lattice" ,r-lattice) |
| 6055 | ("r-mass" ,r-mass) |
| 6056 | ("r-ncdfflow" ,r-ncdfflow) |
| 6057 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 6058 | ("r-rrcov" ,r-rrcov))) |
| 6059 | (home-page "http://www.github.com/RGLab/flowStats") |
| 6060 | (synopsis "Statistical methods for the analysis of flow cytometry data") |
| 6061 | (description |
| 6062 | "This package provides methods and functionality to analyze flow data |
| 6063 | that is beyond the basic infrastructure provided by the @code{flowCore} |
| 6064 | package.") |
| 6065 | (license license:artistic2.0))) |
| 6066 | |
| 6067 | (define-public r-opencyto |
| 6068 | (package |
| 6069 | (name "r-opencyto") |
| 6070 | (version "1.24.0") |
| 6071 | (source |
| 6072 | (origin |
| 6073 | (method url-fetch) |
| 6074 | (uri (bioconductor-uri "openCyto" version)) |
| 6075 | (sha256 |
| 6076 | (base32 |
| 6077 | "0h25nhvq1zq624wsgb55wjcgri9rcd2fnqkb31h9jdakr01dw2sb")))) |
| 6078 | (properties `((upstream-name . "openCyto"))) |
| 6079 | (build-system r-build-system) |
| 6080 | (propagated-inputs |
| 6081 | `(("r-biobase" ,r-biobase) |
| 6082 | ("r-biocgenerics" ,r-biocgenerics) |
| 6083 | ("r-clue" ,r-clue) |
| 6084 | ("r-data-table" ,r-data-table) |
| 6085 | ("r-flowclust" ,r-flowclust) |
| 6086 | ("r-flowcore" ,r-flowcore) |
| 6087 | ("r-flowstats" ,r-flowstats) |
| 6088 | ("r-flowviz" ,r-flowviz) |
| 6089 | ("r-flowworkspace" ,r-flowworkspace) |
| 6090 | ("r-graph" ,r-graph) |
| 6091 | ("r-gtools" ,r-gtools) |
| 6092 | ("r-ks" ,r-ks) |
| 6093 | ("r-lattice" ,r-lattice) |
| 6094 | ("r-mass" ,r-mass) |
| 6095 | ("r-ncdfflow" ,r-ncdfflow) |
| 6096 | ("r-plyr" ,r-plyr) |
| 6097 | ("r-r-utils" ,r-r-utils) |
| 6098 | ("r-rbgl" ,r-rbgl) |
| 6099 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 6100 | ("r-rcpp" ,r-rcpp) |
| 6101 | ("r-rrcov" ,r-rrcov))) |
| 6102 | (home-page "https://bioconductor.org/packages/openCyto") |
| 6103 | (synopsis "Hierarchical gating pipeline for flow cytometry data") |
| 6104 | (description |
| 6105 | "This package is designed to facilitate the automated gating methods in a |
| 6106 | sequential way to mimic the manual gating strategy.") |
| 6107 | (license license:artistic2.0))) |
| 6108 | |
| 6109 | (define-public r-cytoml |
| 6110 | (package |
| 6111 | (name "r-cytoml") |
| 6112 | (version "1.12.1") |
| 6113 | (source |
| 6114 | (origin |
| 6115 | (method url-fetch) |
| 6116 | (uri (bioconductor-uri "CytoML" version)) |
| 6117 | (sha256 |
| 6118 | (base32 |
| 6119 | "0wgi8rwb4spxzd5xvs5amfr5g82ny2nad57j3nmhnhnj1cpirjxz")))) |
| 6120 | (properties `((upstream-name . "CytoML"))) |
| 6121 | (build-system r-build-system) |
| 6122 | (inputs |
| 6123 | `(("libxml2" ,libxml2))) |
| 6124 | (propagated-inputs |
| 6125 | `(("r-base64enc" ,r-base64enc) |
| 6126 | ("r-bh" ,r-bh) |
| 6127 | ("r-biobase" ,r-biobase) |
| 6128 | ("r-corpcor" ,r-corpcor) |
| 6129 | ("r-cytolib" ,r-cytolib) |
| 6130 | ("r-data-table" ,r-data-table) |
| 6131 | ("r-dplyr" ,r-dplyr) |
| 6132 | ("r-flowcore" ,r-flowcore) |
| 6133 | ("r-flowworkspace" ,r-flowworkspace) |
| 6134 | ("r-ggcyto" ,r-ggcyto) |
| 6135 | ("r-graph" ,r-graph) |
| 6136 | ("r-jsonlite" ,r-jsonlite) |
| 6137 | ("r-lattice" ,r-lattice) |
| 6138 | ("r-ncdfflow" ,r-ncdfflow) |
| 6139 | ("r-opencyto" ,r-opencyto) |
| 6140 | ("r-plyr" ,r-plyr) |
| 6141 | ("r-rbgl" ,r-rbgl) |
| 6142 | ("r-rcpp" ,r-rcpp) |
| 6143 | ("r-rcppparallel" ,r-rcppparallel) |
| 6144 | ("r-rgraphviz" ,r-rgraphviz) |
| 6145 | ("r-rprotobuflib" ,r-rprotobuflib) |
| 6146 | ("r-runit" ,r-runit) |
| 6147 | ("r-xml" ,r-xml) |
| 6148 | ("r-yaml" ,r-yaml))) |
| 6149 | (native-inputs |
| 6150 | `(("r-knitr" ,r-knitr))) |
| 6151 | (home-page "https://github.com/RGLab/CytoML") |
| 6152 | (synopsis "GatingML interface for cross platform cytometry data sharing") |
| 6153 | (description |
| 6154 | "This package provides an interface to implementations of the GatingML2.0 |
| 6155 | standard to exchange gated cytometry data with other software platforms.") |
| 6156 | (license license:artistic2.0))) |
| 6157 | |
| 6158 | (define-public r-flowsom |
| 6159 | (package |
| 6160 | (name "r-flowsom") |
| 6161 | (version "1.18.0") |
| 6162 | (source |
| 6163 | (origin |
| 6164 | (method url-fetch) |
| 6165 | (uri (bioconductor-uri "FlowSOM" version)) |
| 6166 | (sha256 |
| 6167 | (base32 |
| 6168 | "0265sq4zvj6d6h5ghqj9xzm4b0z9v65kgyl88cgdcpdkzfnfcvd5")))) |
| 6169 | (properties `((upstream-name . "FlowSOM"))) |
| 6170 | (build-system r-build-system) |
| 6171 | (propagated-inputs |
| 6172 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6173 | ("r-consensusclusterplus" ,r-consensusclusterplus) |
| 6174 | ("r-cytoml" ,r-cytoml) |
| 6175 | ("r-flowcore" ,r-flowcore) |
| 6176 | ("r-flowworkspace" ,r-flowworkspace) |
| 6177 | ("r-igraph" ,r-igraph) |
| 6178 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 6179 | ("r-tsne" ,r-tsne) |
| 6180 | ("r-xml" ,r-xml))) |
| 6181 | (home-page "https://bioconductor.org/packages/FlowSOM/") |
| 6182 | (synopsis "Visualize and interpret cytometry data") |
| 6183 | (description |
| 6184 | "FlowSOM offers visualization options for cytometry data, by using |
| 6185 | self-organizing map clustering and minimal spanning trees.") |
| 6186 | (license license:gpl2+))) |
| 6187 | |
| 6188 | (define-public r-mixomics |
| 6189 | (package |
| 6190 | (name "r-mixomics") |
| 6191 | (version "6.10.9") |
| 6192 | (source |
| 6193 | (origin |
| 6194 | (method url-fetch) |
| 6195 | (uri (bioconductor-uri "mixOmics" version)) |
| 6196 | (sha256 |
| 6197 | (base32 |
| 6198 | "0b457yg8mwqlrn5l344w8qcj8v2ghlj1wdx1ysxbncqvqx7nvgig")))) |
| 6199 | (properties `((upstream-name . "mixOmics"))) |
| 6200 | (build-system r-build-system) |
| 6201 | (propagated-inputs |
| 6202 | `(("r-corpcor" ,r-corpcor) |
| 6203 | ("r-dplyr" ,r-dplyr) |
| 6204 | ("r-ellipse" ,r-ellipse) |
| 6205 | ("r-ggplot2" ,r-ggplot2) |
| 6206 | ("r-gridextra" ,r-gridextra) |
| 6207 | ("r-igraph" ,r-igraph) |
| 6208 | ("r-lattice" ,r-lattice) |
| 6209 | ("r-mass" ,r-mass) |
| 6210 | ("r-matrixstats" ,r-matrixstats) |
| 6211 | ("r-rarpack" ,r-rarpack) |
| 6212 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 6213 | ("r-reshape2" ,r-reshape2) |
| 6214 | ("r-tidyr" ,r-tidyr))) |
| 6215 | (native-inputs |
| 6216 | `(("r-knitr" ,r-knitr))) |
| 6217 | (home-page "http://www.mixOmics.org") |
| 6218 | (synopsis "Multivariate methods for exploration of biological datasets") |
| 6219 | (description |
| 6220 | "mixOmics offers a wide range of multivariate methods for the exploration |
| 6221 | and integration of biological datasets with a particular focus on variable |
| 6222 | selection. The package proposes several sparse multivariate models we have |
| 6223 | developed to identify the key variables that are highly correlated, and/or |
| 6224 | explain the biological outcome of interest. The data that can be analysed |
| 6225 | with mixOmics may come from high throughput sequencing technologies, such as |
| 6226 | omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but |
| 6227 | also beyond the realm of omics (e.g. spectral imaging). The methods |
| 6228 | implemented in mixOmics can also handle missing values without having to |
| 6229 | delete entire rows with missing data.") |
| 6230 | (license license:gpl2+))) |
| 6231 | |
| 6232 | (define-public r-depecher |
| 6233 | (package |
| 6234 | (name "r-depecher") |
| 6235 | (version "1.2.2") |
| 6236 | (source |
| 6237 | (origin |
| 6238 | (method url-fetch) |
| 6239 | (uri (bioconductor-uri "DepecheR" version)) |
| 6240 | (sha256 |
| 6241 | (base32 |
| 6242 | "199j2kw0xnw7y4v1gakm2jgyc7zzlj8xh0570f2yjq55gp1kggbm")))) |
| 6243 | (properties `((upstream-name . "DepecheR"))) |
| 6244 | (build-system r-build-system) |
| 6245 | (propagated-inputs |
| 6246 | `(("r-beanplot" ,r-beanplot) |
| 6247 | ("r-dosnow" ,r-dosnow) |
| 6248 | ("r-dplyr" ,r-dplyr) |
| 6249 | ("r-fnn" ,r-fnn) |
| 6250 | ("r-foreach" ,r-foreach) |
| 6251 | ("r-ggplot2" ,r-ggplot2) |
| 6252 | ("r-gplots" ,r-gplots) |
| 6253 | ("r-mass" ,r-mass) |
| 6254 | ("r-matrixstats" ,r-matrixstats) |
| 6255 | ("r-mixomics" ,r-mixomics) |
| 6256 | ("r-moments" ,r-moments) |
| 6257 | ("r-rcpp" ,r-rcpp) |
| 6258 | ("r-rcppeigen" ,r-rcppeigen) |
| 6259 | ("r-reshape2" ,r-reshape2) |
| 6260 | ("r-robustbase" ,r-robustbase) |
| 6261 | ("r-viridis" ,r-viridis))) |
| 6262 | (native-inputs |
| 6263 | `(("r-knitr" ,r-knitr))) |
| 6264 | (home-page "https://bioconductor.org/packages/DepecheR/") |
| 6265 | (synopsis "Identify traits of clusters in high-dimensional entities") |
| 6266 | (description |
| 6267 | "The purpose of this package is to identify traits in a dataset that can |
| 6268 | separate groups. This is done on two levels. First, clustering is performed, |
| 6269 | using an implementation of sparse K-means. Secondly, the generated clusters |
| 6270 | are used to predict outcomes of groups of individuals based on their |
| 6271 | distribution of observations in the different clusters. As certain clusters |
| 6272 | with separating information will be identified, and these clusters are defined |
| 6273 | by a sparse number of variables, this method can reduce the complexity of |
| 6274 | data, to only emphasize the data that actually matters.") |
| 6275 | (license license:expat))) |
| 6276 | |
| 6277 | (define-public r-rcistarget |
| 6278 | (package |
| 6279 | (name "r-rcistarget") |
| 6280 | (version "1.6.0") |
| 6281 | (source |
| 6282 | (origin |
| 6283 | (method url-fetch) |
| 6284 | (uri (bioconductor-uri "RcisTarget" version)) |
| 6285 | (sha256 |
| 6286 | (base32 |
| 6287 | "1nnah7s0jd24fpfyxsf76jas8dm23c3266aps124wdlqsp9q5qjw")))) |
| 6288 | (properties `((upstream-name . "RcisTarget"))) |
| 6289 | (build-system r-build-system) |
| 6290 | (propagated-inputs |
| 6291 | `(("r-aucell" ,r-aucell) |
| 6292 | ("r-biocgenerics" ,r-biocgenerics) |
| 6293 | ("r-data-table" ,r-data-table) |
| 6294 | ("r-feather" ,r-feather) |
| 6295 | ("r-gseabase" ,r-gseabase) |
| 6296 | ("r-r-utils" ,r-r-utils) |
| 6297 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 6298 | (home-page "https://aertslab.org/#scenic") |
| 6299 | (synopsis "Identify transcription factor binding motifs enriched on a gene list") |
| 6300 | (description |
| 6301 | "RcisTarget identifies @dfn{transcription factor binding motifs} (TFBS) |
| 6302 | over-represented on a gene list. In a first step, RcisTarget selects DNA |
| 6303 | motifs that are significantly over-represented in the surroundings of the |
| 6304 | @dfn{transcription start site} (TSS) of the genes in the gene-set. This is |
| 6305 | achieved by using a database that contains genome-wide cross-species rankings |
| 6306 | for each motif. The motifs that are then annotated to TFs and those that have |
| 6307 | a high @dfn{Normalized Enrichment Score} (NES) are retained. Finally, for |
| 6308 | each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. |
| 6309 | genes in the gene-set that are ranked above the leading edge).") |
| 6310 | (license license:gpl3))) |
| 6311 | |
| 6312 | (define-public r-cicero |
| 6313 | (package |
| 6314 | (name "r-cicero") |
| 6315 | (version "1.4.4") |
| 6316 | (source |
| 6317 | (origin |
| 6318 | (method url-fetch) |
| 6319 | (uri (bioconductor-uri "cicero" version)) |
| 6320 | (sha256 |
| 6321 | (base32 |
| 6322 | "1ay1g2r0la4grcp1y8vcp211lfwzjf7j819ajzdirsh5dab8whld")))) |
| 6323 | (build-system r-build-system) |
| 6324 | (propagated-inputs |
| 6325 | `(("r-assertthat" ,r-assertthat) |
| 6326 | ("r-biobase" ,r-biobase) |
| 6327 | ("r-biocgenerics" ,r-biocgenerics) |
| 6328 | ("r-data-table" ,r-data-table) |
| 6329 | ("r-dplyr" ,r-dplyr) |
| 6330 | ("r-fnn" ,r-fnn) |
| 6331 | ("r-genomicranges" ,r-genomicranges) |
| 6332 | ("r-ggplot2" ,r-ggplot2) |
| 6333 | ("r-glasso" ,r-glasso) |
| 6334 | ("r-gviz" ,r-gviz) |
| 6335 | ("r-igraph" ,r-igraph) |
| 6336 | ("r-iranges" ,r-iranges) |
| 6337 | ("r-matrix" ,r-matrix) |
| 6338 | ("r-monocle" ,r-monocle) |
| 6339 | ("r-plyr" ,r-plyr) |
| 6340 | ("r-reshape2" ,r-reshape2) |
| 6341 | ("r-s4vectors" ,r-s4vectors) |
| 6342 | ("r-stringr" ,r-stringr) |
| 6343 | ("r-tibble" ,r-tibble) |
| 6344 | ("r-tidyr" ,r-tidyr) |
| 6345 | ("r-vgam" ,r-vgam))) |
| 6346 | (native-inputs |
| 6347 | `(("r-knitr" ,r-knitr))) |
| 6348 | (home-page "https://bioconductor.org/packages/cicero/") |
| 6349 | (synopsis "Predict cis-co-accessibility from single-cell data") |
| 6350 | (description |
| 6351 | "Cicero computes putative cis-regulatory maps from single-cell chromatin |
| 6352 | accessibility data. It also extends the monocle package for use in chromatin |
| 6353 | accessibility data.") |
| 6354 | (license license:expat))) |
| 6355 | |
| 6356 | ;; This is the latest commit on the "monocle3" branch. |
| 6357 | (define-public r-cicero-monocle3 |
| 6358 | (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") |
| 6359 | (revision "1")) |
| 6360 | (package (inherit r-cicero) |
| 6361 | (name "r-cicero-monocle3") |
| 6362 | (version (git-version "1.3.2" revision commit)) |
| 6363 | (source |
| 6364 | (origin |
| 6365 | (method git-fetch) |
| 6366 | (uri (git-reference |
| 6367 | (url "https://github.com/cole-trapnell-lab/cicero-release.git") |
| 6368 | (commit commit))) |
| 6369 | (file-name (git-file-name name version)) |
| 6370 | (sha256 |
| 6371 | (base32 |
| 6372 | "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) |
| 6373 | (propagated-inputs |
| 6374 | `(("r-monocle3" ,r-monocle3) |
| 6375 | ,@(alist-delete "r-monocle" |
| 6376 | (package-propagated-inputs r-cicero))))))) |
| 6377 | |
| 6378 | (define-public r-cistopic |
| 6379 | (let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950") |
| 6380 | (revision "0")) |
| 6381 | (package |
| 6382 | (name "r-cistopic") |
| 6383 | (version (git-version "0.2.1" revision commit)) |
| 6384 | (source |
| 6385 | (origin |
| 6386 | (method git-fetch) |
| 6387 | (uri (git-reference |
| 6388 | (url "https://github.com/aertslab/cisTopic.git") |
| 6389 | (commit commit))) |
| 6390 | (file-name (git-file-name name version)) |
| 6391 | (sha256 |
| 6392 | (base32 |
| 6393 | "0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8")))) |
| 6394 | (build-system r-build-system) |
| 6395 | (propagated-inputs |
| 6396 | `(("r-aucell" ,r-aucell) |
| 6397 | ("r-data-table" ,r-data-table) |
| 6398 | ("r-dplyr" ,r-dplyr) |
| 6399 | ("r-dosnow" ,r-dosnow) |
| 6400 | ("r-dt" ,r-dt) |
| 6401 | ("r-feather" ,r-feather) |
| 6402 | ("r-fitdistrplus" ,r-fitdistrplus) |
| 6403 | ("r-genomicranges" ,r-genomicranges) |
| 6404 | ("r-ggplot2" ,r-ggplot2) |
| 6405 | ("r-lda" ,r-lda) |
| 6406 | ("r-matrix" ,r-matrix) |
| 6407 | ("r-plyr" ,r-plyr) |
| 6408 | ("r-rcistarget" ,r-rcistarget) |
| 6409 | ("r-rtracklayer" ,r-rtracklayer) |
| 6410 | ("r-s4vectors" ,r-s4vectors))) |
| 6411 | (home-page "https://github.com/aertslab/cisTopic") |
| 6412 | (synopsis "Modelling of cis-regulatory topics from single cell epigenomics data") |
| 6413 | (description |
| 6414 | "The sparse nature of single cell epigenomics data can be overruled using |
| 6415 | probabilistic modelling methods such as @dfn{Latent Dirichlet |
| 6416 | Allocation} (LDA). This package allows the probabilistic modelling of |
| 6417 | cis-regulatory topics (cisTopics) from single cell epigenomics data, and |
| 6418 | includes functionalities to identify cell states based on the contribution of |
| 6419 | cisTopics and explore the nature and regulatory proteins driving them.") |
| 6420 | (license license:gpl3)))) |
| 6421 | |
| 6422 | (define-public r-genie3 |
| 6423 | (package |
| 6424 | (name "r-genie3") |
| 6425 | (version "1.8.0") |
| 6426 | (source |
| 6427 | (origin |
| 6428 | (method url-fetch) |
| 6429 | (uri (bioconductor-uri "GENIE3" version)) |
| 6430 | (sha256 |
| 6431 | (base32 |
| 6432 | "0p67lhgy3lb4nc958s51hx7rvgwhzwfic9xhpsrask40k43spv7l")))) |
| 6433 | (properties `((upstream-name . "GENIE3"))) |
| 6434 | (build-system r-build-system) |
| 6435 | (propagated-inputs `(("r-reshape2" ,r-reshape2))) |
| 6436 | (home-page "https://bioconductor.org/packages/GENIE3") |
| 6437 | (synopsis "Gene network inference with ensemble of trees") |
| 6438 | (description |
| 6439 | "This package implements the GENIE3 algorithm for inferring gene |
| 6440 | regulatory networks from expression data.") |
| 6441 | (license license:gpl2+))) |
| 6442 | |
| 6443 | (define-public r-roc |
| 6444 | (package |
| 6445 | (name "r-roc") |
| 6446 | (version "1.62.0") |
| 6447 | (source |
| 6448 | (origin |
| 6449 | (method url-fetch) |
| 6450 | (uri (bioconductor-uri "ROC" version)) |
| 6451 | (sha256 |
| 6452 | (base32 |
| 6453 | "1aqpyc28czagg3nbybh55vf152nbar61jjw79w04326d97mc3j3y")))) |
| 6454 | (properties `((upstream-name . "ROC"))) |
| 6455 | (build-system r-build-system) |
| 6456 | (propagated-inputs |
| 6457 | `(("r-knitr" ,r-knitr))) |
| 6458 | (home-page "https://www.bioconductor.org/packages/ROC/") |
| 6459 | (synopsis "Utilities for ROC curves") |
| 6460 | (description |
| 6461 | "This package provides utilities for @dfn{Receiver Operating |
| 6462 | Characteristic} (ROC) curves, with a focus on micro arrays.") |
| 6463 | (license license:artistic2.0))) |
| 6464 | |
| 6465 | (define-public r-illuminahumanmethylation450kanno-ilmn12-hg19 |
| 6466 | (package |
| 6467 | (name "r-illuminahumanmethylation450kanno-ilmn12-hg19") |
| 6468 | (version "0.6.0") |
| 6469 | (source |
| 6470 | (origin |
| 6471 | (method url-fetch) |
| 6472 | (uri (bioconductor-uri |
| 6473 | "IlluminaHumanMethylation450kanno.ilmn12.hg19" |
| 6474 | version 'annotation)) |
| 6475 | (sha256 |
| 6476 | (base32 |
| 6477 | "059vlxsx3p3fcnywwirahsc6mlk813zpqnbv0jsrag6x5bb8z6r4")))) |
| 6478 | (properties |
| 6479 | `((upstream-name |
| 6480 | . "IlluminaHumanMethylation450kanno.ilmn12.hg19"))) |
| 6481 | (build-system r-build-system) |
| 6482 | (propagated-inputs `(("r-minfi" ,r-minfi))) |
| 6483 | (home-page |
| 6484 | "https://bioconductor.org/packages/IlluminaHumanMethylation450kanno.ilmn12.hg19/") |
| 6485 | (synopsis "Annotation for Illumina's 450k methylation arrays") |
| 6486 | (description |
| 6487 | "This package provides manifests and annotation for Illumina's 450k array |
| 6488 | data.") |
| 6489 | (license license:artistic2.0))) |
| 6490 | |
| 6491 | (define-public r-watermelon |
| 6492 | (package |
| 6493 | (name "r-watermelon") |
| 6494 | (version "1.30.0") |
| 6495 | (source |
| 6496 | (origin |
| 6497 | (method url-fetch) |
| 6498 | (uri (bioconductor-uri "wateRmelon" version)) |
| 6499 | (sha256 |
| 6500 | (base32 |
| 6501 | "0a66fq04yph9dis91lzjk9kh134zy6fj98yklrwf24r1080qngx0")))) |
| 6502 | (properties `((upstream-name . "wateRmelon"))) |
| 6503 | (build-system r-build-system) |
| 6504 | (propagated-inputs |
| 6505 | `(("r-biobase" ,r-biobase) |
| 6506 | ("r-illuminahumanmethylation450kanno-ilmn12-hg19" |
| 6507 | ,r-illuminahumanmethylation450kanno-ilmn12-hg19) |
| 6508 | ("r-illuminaio" ,r-illuminaio) |
| 6509 | ("r-limma" ,r-limma) |
| 6510 | ("r-lumi" ,r-lumi) |
| 6511 | ("r-matrixstats" ,r-matrixstats) |
| 6512 | ("r-methylumi" ,r-methylumi) |
| 6513 | ("r-roc" ,r-roc))) |
| 6514 | (home-page "https://bioconductor.org/packages/wateRmelon/") |
| 6515 | (synopsis "Illumina 450 methylation array normalization and metrics") |
| 6516 | (description |
| 6517 | "The standard index of DNA methylation (beta) is computed from methylated |
| 6518 | and unmethylated signal intensities. Betas calculated from raw signal |
| 6519 | intensities perform well, but using 11 methylomic datasets we demonstrate that |
| 6520 | quantile normalization methods produce marked improvement. The commonly used |
| 6521 | procedure of normalizing betas is inferior to the separate normalization of M |
| 6522 | and U, and it is also advantageous to normalize Type I and Type II assays |
| 6523 | separately. This package provides 15 flavours of betas and three performance |
| 6524 | metrics, with methods for objects produced by the @code{methylumi} and |
| 6525 | @code{minfi} packages.") |
| 6526 | (license license:gpl3))) |
| 6527 | |
| 6528 | (define-public r-gdsfmt |
| 6529 | (package |
| 6530 | (name "r-gdsfmt") |
| 6531 | (version "1.22.0") |
| 6532 | (source |
| 6533 | (origin |
| 6534 | (method url-fetch) |
| 6535 | (uri (bioconductor-uri "gdsfmt" version)) |
| 6536 | (sha256 |
| 6537 | (base32 |
| 6538 | "0zc9v62imd0ykz4h30pxa64q0y45qijmkwdk2pd4ncsg8fc2jlz9")) |
| 6539 | (modules '((guix build utils))) |
| 6540 | ;; Remove bundled sources of zlib, lz4, and xz. Don't attempt to build |
| 6541 | ;; them and link with system libraries instead. |
| 6542 | (snippet |
| 6543 | '(begin |
| 6544 | (for-each delete-file-recursively |
| 6545 | '("src/LZ4" |
| 6546 | "src/XZ" |
| 6547 | "src/ZLIB")) |
| 6548 | (substitute* "src/Makevars" |
| 6549 | (("all: \\$\\(SHLIB\\)") "all:") |
| 6550 | (("\\$\\(SHLIB\\): liblzma.a") "") |
| 6551 | (("(ZLIB|LZ4)/.*") "") |
| 6552 | (("CoreArray/dVLIntGDS.cpp.*") |
| 6553 | "CoreArray/dVLIntGDS.cpp") |
| 6554 | (("CoreArray/dVLIntGDS.o.*") |
| 6555 | "CoreArray/dVLIntGDS.o") |
| 6556 | (("PKG_LIBS = ./liblzma.a") |
| 6557 | "PKG_LIBS = -llz4")) |
| 6558 | (substitute* "src/CoreArray/dStream.h" |
| 6559 | (("include \"../(ZLIB|LZ4|XZ/api)/(.*)\"" _ _ header) |
| 6560 | (string-append "include <" header ">"))) |
| 6561 | #t)))) |
| 6562 | (properties `((upstream-name . "gdsfmt"))) |
| 6563 | (build-system r-build-system) |
| 6564 | (inputs |
| 6565 | `(("lz4" ,lz4) |
| 6566 | ("xz" ,xz) |
| 6567 | ("zlib" ,zlib))) |
| 6568 | (home-page "http://corearray.sourceforge.net/") |
| 6569 | (synopsis |
| 6570 | "R Interface to CoreArray Genomic Data Structure (GDS) Files") |
| 6571 | (description |
| 6572 | "This package provides a high-level R interface to CoreArray @dfn{Genomic |
| 6573 | Data Structure} (GDS) data files, which are portable across platforms with |
| 6574 | hierarchical structure to store multiple scalable array-oriented data sets |
| 6575 | with metadata information. It is suited for large-scale datasets, especially |
| 6576 | for data which are much larger than the available random-access memory. The |
| 6577 | @code{gdsfmt} package offers efficient operations specifically designed for |
| 6578 | integers of less than 8 bits, since a diploid genotype, like |
| 6579 | @dfn{single-nucleotide polymorphism} (SNP), usually occupies fewer bits than a |
| 6580 | byte. Data compression and decompression are available with relatively |
| 6581 | efficient random access. It is also allowed to read a GDS file in parallel |
| 6582 | with multiple R processes supported by the package @code{parallel}.") |
| 6583 | (license license:lgpl3))) |
| 6584 | |
| 6585 | (define-public r-bigmelon |
| 6586 | (package |
| 6587 | (name "r-bigmelon") |
| 6588 | (version "1.12.0") |
| 6589 | (source |
| 6590 | (origin |
| 6591 | (method url-fetch) |
| 6592 | (uri (bioconductor-uri "bigmelon" version)) |
| 6593 | (sha256 |
| 6594 | (base32 |
| 6595 | "0sw7rp4p03m1s72b4j06jfb7as3v1n2w2z4ppk8s4f80fb05bcls")))) |
| 6596 | (properties `((upstream-name . "bigmelon"))) |
| 6597 | (build-system r-build-system) |
| 6598 | (propagated-inputs |
| 6599 | `(("r-biobase" ,r-biobase) |
| 6600 | ("r-biocgenerics" ,r-biocgenerics) |
| 6601 | ("r-gdsfmt" ,r-gdsfmt) |
| 6602 | ("r-geoquery" ,r-geoquery) |
| 6603 | ("r-methylumi" ,r-methylumi) |
| 6604 | ("r-minfi" ,r-minfi) |
| 6605 | ("r-watermelon" ,r-watermelon))) |
| 6606 | (home-page "https://bioconductor.org/packages/bigmelon/") |
| 6607 | (synopsis "Illumina methylation array analysis for large experiments") |
| 6608 | (description |
| 6609 | "This package provides methods for working with Illumina arrays using the |
| 6610 | @code{gdsfmt} package.") |
| 6611 | (license license:gpl3))) |
| 6612 | |
| 6613 | (define-public r-seqbias |
| 6614 | (package |
| 6615 | (name "r-seqbias") |
| 6616 | (version "1.34.0") |
| 6617 | (source |
| 6618 | (origin |
| 6619 | (method url-fetch) |
| 6620 | (uri (bioconductor-uri "seqbias" version)) |
| 6621 | (sha256 |
| 6622 | (base32 |
| 6623 | "19vbdyjblij2533ibmrw1n0rkqfrbflma6cg5b79ghks0mg7z8hq")))) |
| 6624 | (properties `((upstream-name . "seqbias"))) |
| 6625 | (build-system r-build-system) |
| 6626 | (propagated-inputs |
| 6627 | `(("r-biostrings" ,r-biostrings) |
| 6628 | ("r-genomicranges" ,r-genomicranges) |
| 6629 | ("r-rhtslib" ,r-rhtslib))) |
| 6630 | (inputs |
| 6631 | `(("zlib" ,zlib))) ; This comes from rhtslib. |
| 6632 | (home-page "https://bioconductor.org/packages/seqbias/") |
| 6633 | (synopsis "Estimation of per-position bias in high-throughput sequencing data") |
| 6634 | (description |
| 6635 | "This package implements a model of per-position sequencing bias in |
| 6636 | high-throughput sequencing data using a simple Bayesian network, the structure |
| 6637 | and parameters of which are trained on a set of aligned reads and a reference |
| 6638 | genome sequence.") |
| 6639 | (license license:lgpl3))) |
| 6640 | |
| 6641 | (define-public r-snplocs-hsapiens-dbsnp144-grch37 |
| 6642 | (package |
| 6643 | (name "r-snplocs-hsapiens-dbsnp144-grch37") |
| 6644 | (version "0.99.20") |
| 6645 | (source (origin |
| 6646 | (method url-fetch) |
| 6647 | (uri (bioconductor-uri "SNPlocs.Hsapiens.dbSNP144.GRCh37" |
| 6648 | version 'annotation)) |
| 6649 | (sha256 |
| 6650 | (base32 |
| 6651 | "1z8kx43ki1jvj7ms7pcybakcdimfwr6zpjvspkjmma97bdz093iz")))) |
| 6652 | (build-system r-build-system) |
| 6653 | ;; As this package provides little more than a very large data file it |
| 6654 | ;; doesn't make sense to build substitutes. |
| 6655 | (arguments `(#:substitutable? #f)) |
| 6656 | (propagated-inputs |
| 6657 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6658 | ("r-s4vectors" ,r-s4vectors) |
| 6659 | ("r-iranges" ,r-iranges) |
| 6660 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6661 | ("r-genomicranges" ,r-genomicranges) |
| 6662 | ("r-bsgenome" ,r-bsgenome) |
| 6663 | ("r-biostrings" ,r-biostrings))) |
| 6664 | (home-page |
| 6665 | "https://bioconductor.org/packages/SNPlocs.Hsapiens.dbSNP144.GRCh37/") |
| 6666 | (synopsis "SNP locations for Homo sapiens (dbSNP Build 144)") |
| 6667 | (description "This package provides SNP locations and alleles for Homo |
| 6668 | sapiens extracted from NCBI dbSNP Build 144. The source data files used for |
| 6669 | this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped |
| 6670 | to reference genome GRCh37.p13. Note that the GRCh37.p13 genome is a |
| 6671 | patched version of GRCh37. However the patch doesn't alter chromosomes 1-22, |
| 6672 | X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for |
| 6673 | the mitochondrion chromosome. Therefore, the SNPs in this package can be |
| 6674 | injected in @code{BSgenome.Hsapiens.UCSC.hg19} and they will land at the |
| 6675 | correct position but this injection will exclude chrM (i.e. nothing will be |
| 6676 | injected in that sequence).") |
| 6677 | (license license:artistic2.0))) |
| 6678 | |
| 6679 | (define-public r-reqon |
| 6680 | (package |
| 6681 | (name "r-reqon") |
| 6682 | (version "1.32.0") |
| 6683 | (source |
| 6684 | (origin |
| 6685 | (method url-fetch) |
| 6686 | (uri (bioconductor-uri "ReQON" version)) |
| 6687 | (sha256 |
| 6688 | (base32 |
| 6689 | "10p6l2zxijqyypdm970jyfqyrnfhaq3nf7cg2q6mgd1srggfa0cx")))) |
| 6690 | (properties `((upstream-name . "ReQON"))) |
| 6691 | (build-system r-build-system) |
| 6692 | (propagated-inputs |
| 6693 | `(("r-rjava" ,r-rjava) |
| 6694 | ("r-rsamtools" ,r-rsamtools) |
| 6695 | ("r-seqbias" ,r-seqbias))) |
| 6696 | (home-page "https://bioconductor.org/packages/ReQON/") |
| 6697 | (synopsis "Recalibrating quality of nucleotides") |
| 6698 | (description |
| 6699 | "This package provides an implementation of an algorithm for |
| 6700 | recalibrating the base quality scores for aligned sequencing data in BAM |
| 6701 | format.") |
| 6702 | (license license:gpl2))) |
| 6703 | |
| 6704 | (define-public r-wavcluster |
| 6705 | (package |
| 6706 | (name "r-wavcluster") |
| 6707 | (version "2.20.0") |
| 6708 | (source |
| 6709 | (origin |
| 6710 | (method url-fetch) |
| 6711 | (uri (bioconductor-uri "wavClusteR" version)) |
| 6712 | (sha256 |
| 6713 | (base32 |
| 6714 | "0vq3xxsvwq86rlya7xc92sc4i6b48sib0pcina3xivg3ky2j3z7y")))) |
| 6715 | (properties `((upstream-name . "wavClusteR"))) |
| 6716 | (build-system r-build-system) |
| 6717 | (propagated-inputs |
| 6718 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6719 | ("r-biostrings" ,r-biostrings) |
| 6720 | ("r-foreach" ,r-foreach) |
| 6721 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 6722 | ("r-genomicranges" ,r-genomicranges) |
| 6723 | ("r-ggplot2" ,r-ggplot2) |
| 6724 | ("r-hmisc" ,r-hmisc) |
| 6725 | ("r-iranges" ,r-iranges) |
| 6726 | ("r-mclust" ,r-mclust) |
| 6727 | ("r-rsamtools" ,r-rsamtools) |
| 6728 | ("r-rtracklayer" ,r-rtracklayer) |
| 6729 | ("r-s4vectors" ,r-s4vectors) |
| 6730 | ("r-seqinr" ,r-seqinr) |
| 6731 | ("r-stringr" ,r-stringr) |
| 6732 | ("r-wmtsa" ,r-wmtsa))) |
| 6733 | (home-page "https://bioconductor.org/packages/wavClusteR/") |
| 6734 | (synopsis "Identification of RNA-protein interaction sites in PAR-CLIP data") |
| 6735 | (description |
| 6736 | "This package provides an integrated pipeline for the analysis of |
| 6737 | PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from |
| 6738 | sequencing errors, SNPs and additional non-experimental sources by a non- |
| 6739 | parametric mixture model. The protein binding sites (clusters) are then |
| 6740 | resolved at high resolution and cluster statistics are estimated using a |
| 6741 | rigorous Bayesian framework. Post-processing of the results, data export for |
| 6742 | UCSC genome browser visualization and motif search analysis are provided. In |
| 6743 | addition, the package integrates RNA-Seq data to estimate the False |
| 6744 | Discovery Rate of cluster detection. Key functions support parallel multicore |
| 6745 | computing. While wavClusteR was designed for PAR-CLIP data analysis, it can |
| 6746 | be applied to the analysis of other NGS data obtained from experimental |
| 6747 | procedures that induce nucleotide substitutions (e.g. BisSeq).") |
| 6748 | (license license:gpl2))) |
| 6749 | |
| 6750 | (define-public r-timeseriesexperiment |
| 6751 | (package |
| 6752 | (name "r-timeseriesexperiment") |
| 6753 | (version "1.4.0") |
| 6754 | (source |
| 6755 | (origin |
| 6756 | (method url-fetch) |
| 6757 | (uri (bioconductor-uri "TimeSeriesExperiment" version)) |
| 6758 | (sha256 |
| 6759 | (base32 |
| 6760 | "0xqa6hzknnci20zx2f6mw5cpqx8pq0v6fzf053hh51p1l2ikvgqm")))) |
| 6761 | (properties |
| 6762 | `((upstream-name . "TimeSeriesExperiment"))) |
| 6763 | (build-system r-build-system) |
| 6764 | (propagated-inputs |
| 6765 | `(("r-deseq2" ,r-deseq2) |
| 6766 | ("r-dplyr" ,r-dplyr) |
| 6767 | ("r-dynamictreecut" ,r-dynamictreecut) |
| 6768 | ("r-edger" ,r-edger) |
| 6769 | ("r-ggplot2" ,r-ggplot2) |
| 6770 | ("r-hmisc" ,r-hmisc) |
| 6771 | ("r-limma" ,r-limma) |
| 6772 | ("r-magrittr" ,r-magrittr) |
| 6773 | ("r-proxy" ,r-proxy) |
| 6774 | ("r-s4vectors" ,r-s4vectors) |
| 6775 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 6776 | ("r-tibble" ,r-tibble) |
| 6777 | ("r-tidyr" ,r-tidyr) |
| 6778 | ("r-vegan" ,r-vegan) |
| 6779 | ("r-viridis" ,r-viridis))) |
| 6780 | (home-page "https://github.com/nlhuong/TimeSeriesExperiment/") |
| 6781 | (synopsis "Analysis for short time-series data") |
| 6782 | (description |
| 6783 | "This package is a visualization and analysis toolbox for short time |
| 6784 | course data which includes dimensionality reduction, clustering, two-sample |
| 6785 | differential expression testing and gene ranking techniques. The package also |
| 6786 | provides methods for retrieving enriched pathways.") |
| 6787 | (license license:lgpl3+))) |
| 6788 | |
| 6789 | (define-public r-variantfiltering |
| 6790 | (package |
| 6791 | (name "r-variantfiltering") |
| 6792 | (version "1.22.0") |
| 6793 | (source |
| 6794 | (origin |
| 6795 | (method url-fetch) |
| 6796 | (uri (bioconductor-uri "VariantFiltering" version)) |
| 6797 | (sha256 |
| 6798 | (base32 |
| 6799 | "13pgfk2mbffd9smmxnwz7g0jrwng78711053wfzadr107zbyn4r8")))) |
| 6800 | (properties |
| 6801 | `((upstream-name . "VariantFiltering"))) |
| 6802 | (build-system r-build-system) |
| 6803 | (propagated-inputs |
| 6804 | `(("r-annotationdbi" ,r-annotationdbi) |
| 6805 | ("r-biobase" ,r-biobase) |
| 6806 | ("r-biocgenerics" ,r-biocgenerics) |
| 6807 | ("r-biocparallel" ,r-biocparallel) |
| 6808 | ("r-biostrings" ,r-biostrings) |
| 6809 | ("r-bsgenome" ,r-bsgenome) |
| 6810 | ("r-dt" ,r-dt) |
| 6811 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 6812 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 6813 | ("r-genomicranges" ,r-genomicranges) |
| 6814 | ("r-genomicscores" ,r-genomicscores) |
| 6815 | ("r-graph" ,r-graph) |
| 6816 | ("r-gviz" ,r-gviz) |
| 6817 | ("r-iranges" ,r-iranges) |
| 6818 | ("r-rbgl" ,r-rbgl) |
| 6819 | ("r-rsamtools" ,r-rsamtools) |
| 6820 | ("r-s4vectors" ,r-s4vectors) |
| 6821 | ("r-shiny" ,r-shiny) |
| 6822 | ("r-shinyjs" ,r-shinyjs) |
| 6823 | ("r-shinythemes" ,r-shinythemes) |
| 6824 | ("r-shinytree" ,r-shinytree) |
| 6825 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 6826 | ("r-variantannotation" ,r-variantannotation) |
| 6827 | ("r-xvector" ,r-xvector))) |
| 6828 | (home-page "https://github.com/rcastelo/VariantFiltering") |
| 6829 | (synopsis "Filtering of coding and non-coding genetic variants") |
| 6830 | (description |
| 6831 | "Filter genetic variants using different criteria such as inheritance |
| 6832 | model, amino acid change consequence, minor allele frequencies across human |
| 6833 | populations, splice site strength, conservation, etc.") |
| 6834 | (license license:artistic2.0))) |
| 6835 | |
| 6836 | (define-public r-genomegraphs |
| 6837 | (package |
| 6838 | (name "r-genomegraphs") |
| 6839 | (version "1.46.0") |
| 6840 | (source |
| 6841 | (origin |
| 6842 | (method url-fetch) |
| 6843 | (uri (bioconductor-uri "GenomeGraphs" version)) |
| 6844 | (sha256 |
| 6845 | (base32 |
| 6846 | "05vavhz936v7cknig2f2mn3fd9fiy54r3swlvifpawramblp1ags")))) |
| 6847 | (properties `((upstream-name . "GenomeGraphs"))) |
| 6848 | (build-system r-build-system) |
| 6849 | (propagated-inputs |
| 6850 | `(("r-biomart" ,r-biomart))) |
| 6851 | (home-page "https://bioconductor.org/packages/GenomeGraphs/") |
| 6852 | (synopsis "Plotting genomic information from Ensembl") |
| 6853 | (description |
| 6854 | "Genomic data analyses requires integrated visualization of known genomic |
| 6855 | information and new experimental data. GenomeGraphs uses the biomaRt package |
| 6856 | to perform live annotation queries to Ensembl and translates this to e.g. |
| 6857 | gene/transcript structures in viewports of the grid graphics package. This |
| 6858 | results in genomic information plotted together with your data. Another |
| 6859 | strength of GenomeGraphs is to plot different data types such as array CGH, |
| 6860 | gene expression, sequencing and other data, together in one plot using the |
| 6861 | same genome coordinate system.") |
| 6862 | (license license:artistic2.0))) |
| 6863 | |
| 6864 | (define-public r-wavetiling |
| 6865 | (package |
| 6866 | (name "r-wavetiling") |
| 6867 | (version "1.28.0") |
| 6868 | (source |
| 6869 | (origin |
| 6870 | (method url-fetch) |
| 6871 | (uri (bioconductor-uri "waveTiling" version)) |
| 6872 | (sha256 |
| 6873 | (base32 |
| 6874 | "0d7l559zlmly8mncmh1zhkqmsml0bwwfpm7ccp8l26y852vwf7hf")))) |
| 6875 | (properties `((upstream-name . "waveTiling"))) |
| 6876 | (build-system r-build-system) |
| 6877 | (propagated-inputs |
| 6878 | `(("r-affy" ,r-affy) |
| 6879 | ("r-biobase" ,r-biobase) |
| 6880 | ("r-biostrings" ,r-biostrings) |
| 6881 | ("r-genomegraphs" ,r-genomegraphs) |
| 6882 | ("r-genomicranges" ,r-genomicranges) |
| 6883 | ("r-iranges" ,r-iranges) |
| 6884 | ("r-oligo" ,r-oligo) |
| 6885 | ("r-oligoclasses" ,r-oligoclasses) |
| 6886 | ("r-preprocesscore" ,r-preprocesscore) |
| 6887 | ("r-waveslim" ,r-waveslim))) |
| 6888 | (home-page "https://r-forge.r-project.org/projects/wavetiling/") |
| 6889 | (synopsis "Wavelet-based models for tiling array transcriptome analysis") |
| 6890 | (description |
| 6891 | "This package is designed to conduct transcriptome analysis for tiling |
| 6892 | arrays based on fast wavelet-based functional models.") |
| 6893 | (license license:gpl2+))) |
| 6894 | |
| 6895 | (define-public r-variancepartition |
| 6896 | (package |
| 6897 | (name "r-variancepartition") |
| 6898 | (version "1.16.1") |
| 6899 | (source |
| 6900 | (origin |
| 6901 | (method url-fetch) |
| 6902 | (uri (bioconductor-uri "variancePartition" version)) |
| 6903 | (sha256 |
| 6904 | (base32 |
| 6905 | "02pzsff14j4am2d949mh8xgi0c7k44g09q4lr6nqm08vf92brb6g")))) |
| 6906 | (properties |
| 6907 | `((upstream-name . "variancePartition"))) |
| 6908 | (build-system r-build-system) |
| 6909 | (propagated-inputs |
| 6910 | `(("r-biobase" ,r-biobase) |
| 6911 | ("r-biocparallel" ,r-biocparallel) |
| 6912 | ("r-colorramps" ,r-colorramps) |
| 6913 | ("r-doparallel" ,r-doparallel) |
| 6914 | ("r-foreach" ,r-foreach) |
| 6915 | ("r-ggplot2" ,r-ggplot2) |
| 6916 | ("r-gplots" ,r-gplots) |
| 6917 | ("r-iterators" ,r-iterators) |
| 6918 | ("r-limma" ,r-limma) |
| 6919 | ("r-lme4" ,r-lme4) |
| 6920 | ("r-lmertest" ,r-lmertest) |
| 6921 | ("r-mass" ,r-mass) |
| 6922 | ("r-pbkrtest" ,r-pbkrtest) |
| 6923 | ("r-progress" ,r-progress) |
| 6924 | ("r-reshape2" ,r-reshape2) |
| 6925 | ("r-scales" ,r-scales))) |
| 6926 | (home-page "https://bioconductor.org/packages/variancePartition/") |
| 6927 | (synopsis "Analyze variation in gene expression experiments") |
| 6928 | (description |
| 6929 | "This is a package providing tools to quantify and interpret multiple |
| 6930 | sources of biological and technical variation in gene expression experiments. |
| 6931 | It uses a linear mixed model to quantify variation in gene expression |
| 6932 | attributable to individual, tissue, time point, or technical variables. The |
| 6933 | package includes dream differential expression analysis for repeated |
| 6934 | measures.") |
| 6935 | (license license:gpl2+))) |
| 6936 | |
| 6937 | (define-public r-htqpcr |
| 6938 | (package |
| 6939 | (name "r-htqpcr") |
| 6940 | (version "1.40.0") |
| 6941 | (source |
| 6942 | (origin |
| 6943 | (method url-fetch) |
| 6944 | (uri (bioconductor-uri "HTqPCR" version)) |
| 6945 | (sha256 |
| 6946 | (base32 |
| 6947 | "008iczqaa0wn5nw144vfg3qylg7qa1q963nq9mqhgj3sxlg4rmjx")))) |
| 6948 | (properties `((upstream-name . "HTqPCR"))) |
| 6949 | (build-system r-build-system) |
| 6950 | (propagated-inputs |
| 6951 | `(("r-affy" ,r-affy) |
| 6952 | ("r-biobase" ,r-biobase) |
| 6953 | ("r-gplots" ,r-gplots) |
| 6954 | ("r-limma" ,r-limma) |
| 6955 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 6956 | (home-page (string-append "https://www.ebi.ac.uk/sites/ebi.ac.uk/files/" |
| 6957 | "groups/bertone/software/HTqPCR.pdf")) |
| 6958 | (synopsis "Automated analysis of high-throughput qPCR data") |
| 6959 | (description |
| 6960 | "Analysis of Ct values from high throughput quantitative real-time |
| 6961 | PCR (qPCR) assays across multiple conditions or replicates. The input data |
| 6962 | can be from spatially-defined formats such ABI TaqMan Low Density Arrays or |
| 6963 | OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad |
| 6964 | Laboratories; conventional 96- or 384-well plates; or microfluidic devices |
| 6965 | such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data |
| 6966 | loading, quality assessment, normalization, visualization and parametric or |
| 6967 | non-parametric testing for statistical significance in Ct values between |
| 6968 | features (e.g. genes, microRNAs).") |
| 6969 | (license license:artistic2.0))) |
| 6970 | |
| 6971 | (define-public r-unifiedwmwqpcr |
| 6972 | (package |
| 6973 | (name "r-unifiedwmwqpcr") |
| 6974 | (version "1.22.0") |
| 6975 | (source |
| 6976 | (origin |
| 6977 | (method url-fetch) |
| 6978 | (uri (bioconductor-uri "unifiedWMWqPCR" version)) |
| 6979 | (sha256 |
| 6980 | (base32 |
| 6981 | "1l6rf7scxxyz4x0m4li54y6905sqj4jrx481zb9h3vqhcfcmn8lj")))) |
| 6982 | (properties |
| 6983 | `((upstream-name . "unifiedWMWqPCR"))) |
| 6984 | (build-system r-build-system) |
| 6985 | (propagated-inputs |
| 6986 | `(("r-biocgenerics" ,r-biocgenerics) |
| 6987 | ("r-htqpcr" ,r-htqpcr))) |
| 6988 | (home-page "https://bioconductor.org/packages/unifiedWMWqPCR") |
| 6989 | (synopsis "Unified Wilcoxon-Mann Whitney Test for differential expression in qPCR data") |
| 6990 | (description |
| 6991 | "This package implements the unified Wilcoxon-Mann-Whitney Test for qPCR |
| 6992 | data. This modified test allows for testing differential expression in qPCR |
| 6993 | data.") |
| 6994 | (license license:gpl2+))) |
| 6995 | |
| 6996 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put |
| 6997 | ;; it here. |
| 6998 | (define-public r-activedriverwgs |
| 6999 | (package |
| 7000 | (name "r-activedriverwgs") |
| 7001 | (version "1.0.1") |
| 7002 | (source |
| 7003 | (origin |
| 7004 | (method url-fetch) |
| 7005 | (uri (cran-uri "ActiveDriverWGS" version)) |
| 7006 | (sha256 |
| 7007 | (base32 |
| 7008 | "08l9dj8d3cd74z1dqn8n4yqykwvqjxsfa067wnxyh7xnfvvnm5v1")))) |
| 7009 | (properties |
| 7010 | `((upstream-name . "ActiveDriverWGS"))) |
| 7011 | (build-system r-build-system) |
| 7012 | (propagated-inputs |
| 7013 | `(("r-biostrings" ,r-biostrings) |
| 7014 | ("r-bsgenome" ,r-bsgenome) |
| 7015 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 7016 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 7017 | ("r-genomicranges" ,r-genomicranges) |
| 7018 | ("r-iranges" ,r-iranges) |
| 7019 | ("r-plyr" ,r-plyr) |
| 7020 | ("r-s4vectors" ,r-s4vectors))) |
| 7021 | (home-page "https://cran.r-project.org/web/packages/ActiveDriverWGS/") |
| 7022 | (synopsis "Driver discovery tool for cancer whole genomes") |
| 7023 | (description |
| 7024 | "This package provides a method for finding an enrichment of cancer |
| 7025 | simple somatic mutations (SNVs and Indels) in functional elements across the |
| 7026 | human genome. ActiveDriverWGS detects coding and noncoding driver elements |
| 7027 | using whole genome sequencing data.") |
| 7028 | (license license:gpl3))) |
| 7029 | |
| 7030 | ;; This is a CRAN package, but it depends on Bioconductor packages, so we put |
| 7031 | ;; it here. |
| 7032 | (define-public r-activepathways |
| 7033 | (package |
| 7034 | (name "r-activepathways") |
| 7035 | (version "1.0.1") |
| 7036 | (source |
| 7037 | (origin |
| 7038 | (method url-fetch) |
| 7039 | (uri (cran-uri "ActivePathways" version)) |
| 7040 | (sha256 |
| 7041 | (base32 |
| 7042 | "1xb0d1svmzw404pv8ja6wr4773k7x2lxkrzrayilvzqbfzj1wx20")))) |
| 7043 | (properties |
| 7044 | `((upstream-name . "ActivePathways"))) |
| 7045 | (build-system r-build-system) |
| 7046 | (propagated-inputs |
| 7047 | `(("r-data-table" ,r-data-table) |
| 7048 | ("r-ggplot2" ,r-ggplot2) |
| 7049 | ("r-metap" ,r-metap))) |
| 7050 | (native-inputs |
| 7051 | `(("r-knitr" ,r-knitr))) |
| 7052 | (home-page "https://cran.r-project.org/web/packages/ActivePathways/") |
| 7053 | (synopsis "Multivariate pathway enrichment analysis") |
| 7054 | (description |
| 7055 | "This package represents an integrative method of analyzing multi omics |
| 7056 | data that conducts enrichment analysis of annotated gene sets. ActivePathways |
| 7057 | uses a statistical data fusion approach, rationalizes contributing evidence |
| 7058 | and highlights associated genes, improving systems-level understanding of |
| 7059 | cellular organization in health and disease.") |
| 7060 | (license license:gpl3))) |
| 7061 | |
| 7062 | (define-public r-bgmix |
| 7063 | (package |
| 7064 | (name "r-bgmix") |
| 7065 | (version "1.46.0") |
| 7066 | (source |
| 7067 | (origin |
| 7068 | (method url-fetch) |
| 7069 | (uri (bioconductor-uri "BGmix" version)) |
| 7070 | (sha256 |
| 7071 | (base32 |
| 7072 | "1bwqqhkh4m3hhpd71grwjrg7n07lzvys4y7aghmw2gw5ibnk5683")))) |
| 7073 | (properties `((upstream-name . "BGmix"))) |
| 7074 | (build-system r-build-system) |
| 7075 | (propagated-inputs |
| 7076 | `(("r-kernsmooth" ,r-kernsmooth))) |
| 7077 | (home-page "https://bioconductor.org/packages/BGmix/") |
| 7078 | (synopsis "Bayesian models for differential gene expression") |
| 7079 | (description |
| 7080 | "This package provides fully Bayesian mixture models for differential |
| 7081 | gene expression.") |
| 7082 | (license license:gpl2))) |
| 7083 | |
| 7084 | (define-public r-bgx |
| 7085 | (package |
| 7086 | (name "r-bgx") |
| 7087 | (version "1.52.0") |
| 7088 | (source |
| 7089 | (origin |
| 7090 | (method url-fetch) |
| 7091 | (uri (bioconductor-uri "bgx" version)) |
| 7092 | (sha256 |
| 7093 | (base32 |
| 7094 | "0fiqqv6pin0zhxaw67hzfjccq2qkl9qfqjf10nx2zmpxm2licavm")))) |
| 7095 | (properties `((upstream-name . "bgx"))) |
| 7096 | (build-system r-build-system) |
| 7097 | (propagated-inputs |
| 7098 | `(("r-affy" ,r-affy) |
| 7099 | ("r-biobase" ,r-biobase) |
| 7100 | ("r-gcrma" ,r-gcrma) |
| 7101 | ("r-rcpp" ,r-rcpp))) |
| 7102 | (home-page "https://bioconductor.org/packages/bgx/") |
| 7103 | (synopsis "Bayesian gene expression") |
| 7104 | (description |
| 7105 | "This package provides tools for Bayesian integrated analysis of |
| 7106 | Affymetrix GeneChips.") |
| 7107 | (license license:gpl2))) |
| 7108 | |
| 7109 | (define-public r-bhc |
| 7110 | (package |
| 7111 | (name "r-bhc") |
| 7112 | (version "1.38.0") |
| 7113 | (source |
| 7114 | (origin |
| 7115 | (method url-fetch) |
| 7116 | (uri (bioconductor-uri "BHC" version)) |
| 7117 | (sha256 |
| 7118 | (base32 |
| 7119 | "1bxx3jak8mgvay3j1xd59bb9j86pzl6hh5abxww9x1b7rswmy1jh")))) |
| 7120 | (properties `((upstream-name . "BHC"))) |
| 7121 | (build-system r-build-system) |
| 7122 | (home-page "https://bioconductor.org/packages/BHC/") |
| 7123 | (synopsis "Bayesian hierarchical clustering") |
| 7124 | (description |
| 7125 | "The method implemented in this package performs bottom-up hierarchical |
| 7126 | clustering, using a Dirichlet Process (infinite mixture) to model uncertainty |
| 7127 | in the data and Bayesian model selection to decide at each step which clusters |
| 7128 | to merge. This avoids several limitations of traditional methods, for example |
| 7129 | how many clusters there should be and how to choose a principled distance |
| 7130 | metric. This implementation accepts multinomial (i.e. discrete, with 2+ |
| 7131 | categories) or time-series data. This version also includes a randomised |
| 7132 | algorithm which is more efficient for larger data sets.") |
| 7133 | (license license:gpl3))) |
| 7134 | |
| 7135 | (define-public r-bicare |
| 7136 | (package |
| 7137 | (name "r-bicare") |
| 7138 | (version "1.44.0") |
| 7139 | (source |
| 7140 | (origin |
| 7141 | (method url-fetch) |
| 7142 | (uri (bioconductor-uri "BicARE" version)) |
| 7143 | (sha256 |
| 7144 | (base32 |
| 7145 | "1gia5vzmvbk4k1vx3bh9nld1ws9s3c0y11qfbzqhfnfjbd7n8qcs")))) |
| 7146 | (properties `((upstream-name . "BicARE"))) |
| 7147 | (build-system r-build-system) |
| 7148 | (propagated-inputs |
| 7149 | `(("r-biobase" ,r-biobase) |
| 7150 | ("r-gseabase" ,r-gseabase) |
| 7151 | ("r-multtest" ,r-multtest))) |
| 7152 | (home-page "http://bioinfo.curie.fr") |
| 7153 | (synopsis "Biclustering analysis and results exploration") |
| 7154 | (description |
| 7155 | "This is a package for biclustering analysis and exploration of |
| 7156 | results.") |
| 7157 | (license license:gpl2))) |
| 7158 | |
| 7159 | (define-public r-bifet |
| 7160 | (package |
| 7161 | (name "r-bifet") |
| 7162 | (version "1.6.0") |
| 7163 | (source |
| 7164 | (origin |
| 7165 | (method url-fetch) |
| 7166 | (uri (bioconductor-uri "BiFET" version)) |
| 7167 | (sha256 |
| 7168 | (base32 |
| 7169 | "0ck1d6hxd4f40hfz8p2z5xmjbz79yhrf6fisjka2xzk5v9fm4p4k")))) |
| 7170 | (properties `((upstream-name . "BiFET"))) |
| 7171 | (build-system r-build-system) |
| 7172 | (propagated-inputs |
| 7173 | `(("r-genomicranges" ,r-genomicranges) |
| 7174 | ("r-poibin" ,r-poibin))) |
| 7175 | (home-page "https://bioconductor.org/packages/BiFET") |
| 7176 | (synopsis "Bias-free footprint enrichment test") |
| 7177 | (description |
| 7178 | "BiFET identifies @dfn{transcription factors} (TFs) whose footprints are |
| 7179 | over-represented in target regions compared to background regions after |
| 7180 | correcting for the bias arising from the imbalance in read counts and GC |
| 7181 | contents between the target and background regions. For a given TF k, BiFET |
| 7182 | tests the null hypothesis that the target regions have the same probability of |
| 7183 | having footprints for the TF k as the background regions while correcting for |
| 7184 | the read count and GC content bias.") |
| 7185 | (license license:gpl3))) |
| 7186 | |
| 7187 | (define-public r-rsbml |
| 7188 | (package |
| 7189 | (name "r-rsbml") |
| 7190 | (version "2.44.0") |
| 7191 | (source |
| 7192 | (origin |
| 7193 | (method url-fetch) |
| 7194 | (uri (bioconductor-uri "rsbml" version)) |
| 7195 | (sha256 |
| 7196 | (base32 |
| 7197 | "1dbp0aaijxn3na26b68ws0v9qzvml61ifb9z4i8pz7q6h48n7lxa")))) |
| 7198 | (properties `((upstream-name . "rsbml"))) |
| 7199 | (build-system r-build-system) |
| 7200 | (inputs |
| 7201 | `(("libsbml" ,libsbml) |
| 7202 | ("zlib" ,zlib))) |
| 7203 | (propagated-inputs |
| 7204 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7205 | ("r-graph" ,r-graph))) |
| 7206 | (native-inputs |
| 7207 | `(("pkg-config" ,pkg-config))) |
| 7208 | (home-page "http://www.sbml.org") |
| 7209 | (synopsis "R support for SBML") |
| 7210 | (description |
| 7211 | "This package provides an R interface to libsbml for SBML parsing, |
| 7212 | validating output, provides an S4 SBML DOM, converts SBML to R graph objects.") |
| 7213 | (license license:artistic2.0))) |
| 7214 | |
| 7215 | (define-public r-hypergraph |
| 7216 | (package |
| 7217 | (name "r-hypergraph") |
| 7218 | (version "1.58.0") |
| 7219 | (source |
| 7220 | (origin |
| 7221 | (method url-fetch) |
| 7222 | (uri (bioconductor-uri "hypergraph" version)) |
| 7223 | (sha256 |
| 7224 | (base32 |
| 7225 | "1bixmslxy7r987zw1vf4dg72hfi04lf4vj03n7ygym2g8nfhbh7m")))) |
| 7226 | (properties `((upstream-name . "hypergraph"))) |
| 7227 | (build-system r-build-system) |
| 7228 | (propagated-inputs |
| 7229 | `(("r-graph" ,r-graph))) |
| 7230 | (home-page "https://bioconductor.org/packages/hypergraph") |
| 7231 | (synopsis "Hypergraph data structures") |
| 7232 | (description |
| 7233 | "This package implements some simple capabilities for representing and |
| 7234 | manipulating hypergraphs.") |
| 7235 | (license license:artistic2.0))) |
| 7236 | |
| 7237 | (define-public r-hyperdraw |
| 7238 | (package |
| 7239 | (name "r-hyperdraw") |
| 7240 | (version "1.38.0") |
| 7241 | (source |
| 7242 | (origin |
| 7243 | (method url-fetch) |
| 7244 | (uri (bioconductor-uri "hyperdraw" version)) |
| 7245 | (sha256 |
| 7246 | (base32 |
| 7247 | "0a8h3pb7196qi49ady8ni92m5wqb1hvxw6khk9j63mwj3h7jinbj")))) |
| 7248 | (properties `((upstream-name . "hyperdraw"))) |
| 7249 | (build-system r-build-system) |
| 7250 | (inputs `(("graphviz" ,graphviz))) |
| 7251 | (propagated-inputs |
| 7252 | `(("r-graph" ,r-graph) |
| 7253 | ("r-hypergraph" ,r-hypergraph) |
| 7254 | ("r-rgraphviz" ,r-rgraphviz))) |
| 7255 | (home-page "https://bioconductor.org/packages/hyperdraw") |
| 7256 | (synopsis "Visualizing hypergraphs") |
| 7257 | (description |
| 7258 | "This package provides functions for visualizing hypergraphs.") |
| 7259 | (license license:gpl2+))) |
| 7260 | |
| 7261 | (define-public r-biggr |
| 7262 | (package |
| 7263 | (name "r-biggr") |
| 7264 | (version "1.22.0") |
| 7265 | (source |
| 7266 | (origin |
| 7267 | (method url-fetch) |
| 7268 | (uri (bioconductor-uri "BiGGR" version)) |
| 7269 | (sha256 |
| 7270 | (base32 |
| 7271 | "1n2ypc84abmhn6br0yi87k7lvjc11k7abzhgvzdabc2ai1qgcqif")))) |
| 7272 | (properties `((upstream-name . "BiGGR"))) |
| 7273 | (build-system r-build-system) |
| 7274 | (propagated-inputs |
| 7275 | `(("r-hyperdraw" ,r-hyperdraw) |
| 7276 | ("r-hypergraph" ,r-hypergraph) |
| 7277 | ("r-lim" ,r-lim) |
| 7278 | ("r-limsolve" ,r-limsolve) |
| 7279 | ("r-rsbml" ,r-rsbml) |
| 7280 | ("r-stringr" ,r-stringr))) |
| 7281 | (home-page "https://bioconductor.org/packages/BiGGR/") |
| 7282 | (synopsis "Constraint based modeling using metabolic reconstruction databases") |
| 7283 | (description |
| 7284 | "This package provides an interface to simulate metabolic reconstruction |
| 7285 | from the @url{http://bigg.ucsd.edu/, BiGG database} and other metabolic |
| 7286 | reconstruction databases. The package facilitates @dfn{flux balance |
| 7287 | analysis} (FBA) and the sampling of feasible flux distributions. Metabolic |
| 7288 | networks and estimated fluxes can be visualized with hypergraphs.") |
| 7289 | (license license:gpl3+))) |
| 7290 | |
| 7291 | (define-public r-bigmemoryextras |
| 7292 | (package |
| 7293 | (name "r-bigmemoryextras") |
| 7294 | (version "1.34.0") |
| 7295 | (source |
| 7296 | (origin |
| 7297 | (method url-fetch) |
| 7298 | (uri (bioconductor-uri "bigmemoryExtras" version)) |
| 7299 | (sha256 |
| 7300 | (base32 |
| 7301 | "17dk7c44ikphcrpi8hnxyvlmj30qmj098kc0ihfi69bp9rw1cibq")))) |
| 7302 | (properties |
| 7303 | `((upstream-name . "bigmemoryExtras"))) |
| 7304 | (build-system r-build-system) |
| 7305 | (propagated-inputs |
| 7306 | `(("r-bigmemory" ,r-bigmemory))) |
| 7307 | (home-page "https://github.com/phaverty/bigmemoryExtras") |
| 7308 | (synopsis "Extension of the bigmemory package") |
| 7309 | (description |
| 7310 | "This package defines a @code{BigMatrix} @code{ReferenceClass} which adds |
| 7311 | safety and convenience features to the @code{filebacked.big.matrix} class from |
| 7312 | the @code{bigmemory} package. @code{BigMatrix} protects against segfaults by |
| 7313 | monitoring and gracefully restoring the connection to on-disk data and it also |
| 7314 | protects against accidental data modification with a filesystem-based |
| 7315 | permissions system. Utilities are provided for using @code{BigMatrix}-derived |
| 7316 | classes as @code{assayData} matrices within the @code{Biobase} package's |
| 7317 | @code{eSet} family of classes. @code{BigMatrix} provides some optimizations |
| 7318 | related to attaching to, and indexing into, file-backed matrices with |
| 7319 | dimnames. Additionally, the package provides a @code{BigMatrixFactor} class, |
| 7320 | a file-backed matrix with factor properties.") |
| 7321 | (license license:artistic2.0))) |
| 7322 | |
| 7323 | (define-public r-bigpint |
| 7324 | (package |
| 7325 | (name "r-bigpint") |
| 7326 | (version "1.2.2") |
| 7327 | (source |
| 7328 | (origin |
| 7329 | (method url-fetch) |
| 7330 | (uri (bioconductor-uri "bigPint" version)) |
| 7331 | (sha256 |
| 7332 | (base32 |
| 7333 | "1zkakxi1iqavzmjxnkkd02qm5jk28ldcvcdcxaafz748dz6s67fs")))) |
| 7334 | (properties `((upstream-name . "bigPint"))) |
| 7335 | (build-system r-build-system) |
| 7336 | (propagated-inputs |
| 7337 | `(("r-dplyr" ,r-dplyr) |
| 7338 | ("r-ggally" ,r-ggally) |
| 7339 | ("r-ggplot2" ,r-ggplot2) |
| 7340 | ("r-gridextra" ,r-gridextra) |
| 7341 | ("r-hexbin" ,r-hexbin) |
| 7342 | ("r-hmisc" ,r-hmisc) |
| 7343 | ("r-htmlwidgets" ,r-htmlwidgets) |
| 7344 | ("r-plotly" ,r-plotly) |
| 7345 | ("r-plyr" ,r-plyr) |
| 7346 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 7347 | ("r-reshape" ,r-reshape) |
| 7348 | ("r-shiny" ,r-shiny) |
| 7349 | ("r-shinycssloaders" ,r-shinycssloaders) |
| 7350 | ("r-shinydashboard" ,r-shinydashboard) |
| 7351 | ("r-stringr" ,r-stringr) |
| 7352 | ("r-tidyr" ,r-tidyr))) |
| 7353 | (native-inputs |
| 7354 | `(("r-knitr" ,r-knitr))) |
| 7355 | (home-page "https://github.com/lindsayrutter/bigPint") |
| 7356 | (synopsis "Big multivariate data plotted interactively") |
| 7357 | (description |
| 7358 | "This package provides methods for visualizing large multivariate |
| 7359 | datasets using static and interactive scatterplot matrices, parallel |
| 7360 | coordinate plots, volcano plots, and litre plots. It includes examples for |
| 7361 | visualizing RNA-sequencing datasets and differentially expressed genes.") |
| 7362 | (license license:gpl3))) |
| 7363 | |
| 7364 | (define-public r-chemminer |
| 7365 | (package |
| 7366 | (name "r-chemminer") |
| 7367 | (version "3.38.0") |
| 7368 | (source |
| 7369 | (origin |
| 7370 | (method url-fetch) |
| 7371 | (uri (bioconductor-uri "ChemmineR" version)) |
| 7372 | (sha256 |
| 7373 | (base32 |
| 7374 | "1j6vmkhc03dmmkm5wgbcv62pw5dclp49f906xkx1pwg27bdldbga")))) |
| 7375 | (properties `((upstream-name . "ChemmineR"))) |
| 7376 | (build-system r-build-system) |
| 7377 | (propagated-inputs |
| 7378 | `(("r-base64enc" ,r-base64enc) |
| 7379 | ("r-bh" ,r-bh) |
| 7380 | ("r-biocgenerics" ,r-biocgenerics) |
| 7381 | ("r-dbi" ,r-dbi) |
| 7382 | ("r-digest" ,r-digest) |
| 7383 | ("r-dt" ,r-dt) |
| 7384 | ("r-ggplot2" ,r-ggplot2) |
| 7385 | ("r-gridextra" ,r-gridextra) |
| 7386 | ("r-png" ,r-png) |
| 7387 | ("r-rcpp" ,r-rcpp) |
| 7388 | ("r-rcurl" ,r-rcurl) |
| 7389 | ("r-rjson" ,r-rjson) |
| 7390 | ("r-rsvg" ,r-rsvg))) |
| 7391 | (home-page "https://github.com/girke-lab/ChemmineR") |
| 7392 | (synopsis "Cheminformatics toolkit for R") |
| 7393 | (description |
| 7394 | "ChemmineR is a cheminformatics package for analyzing drug-like small |
| 7395 | molecule data in R. It contains functions for efficient processing of large |
| 7396 | numbers of molecules, physicochemical/structural property predictions, |
| 7397 | structural similarity searching, classification and clustering of compound |
| 7398 | libraries with a wide spectrum of algorithms. In addition, it offers |
| 7399 | visualization functions for compound clustering results and chemical |
| 7400 | structures.") |
| 7401 | (license license:artistic2.0))) |
| 7402 | |
| 7403 | (define-public r-bioassayr |
| 7404 | (package |
| 7405 | (name "r-bioassayr") |
| 7406 | (version "1.24.0") |
| 7407 | (source |
| 7408 | (origin |
| 7409 | (method url-fetch) |
| 7410 | (uri (bioconductor-uri "bioassayR" version)) |
| 7411 | (sha256 |
| 7412 | (base32 |
| 7413 | "08vxkvxhqnryfbj4dwk3ifb9pn544www9zk2pj9fjbh5xfpwi7zw")))) |
| 7414 | (properties `((upstream-name . "bioassayR"))) |
| 7415 | (build-system r-build-system) |
| 7416 | (propagated-inputs |
| 7417 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7418 | ("r-chemminer" ,r-chemminer) |
| 7419 | ("r-dbi" ,r-dbi) |
| 7420 | ("r-matrix" ,r-matrix) |
| 7421 | ("r-rjson" ,r-rjson) |
| 7422 | ("r-rsqlite" ,r-rsqlite) |
| 7423 | ("r-xml" ,r-xml))) |
| 7424 | (native-inputs |
| 7425 | `(("r-knitr" ,r-knitr))) |
| 7426 | (home-page "https://github.com/TylerBackman/bioassayR") |
| 7427 | (synopsis "Cross-target analysis of small molecule bioactivity") |
| 7428 | (description |
| 7429 | "bioassayR is a computational tool that enables simultaneous analysis of |
| 7430 | thousands of bioassay experiments performed over a diverse set of compounds |
| 7431 | and biological targets. Unique features include support for large-scale |
| 7432 | cross-target analyses of both public and custom bioassays, generation of |
| 7433 | @dfn{high throughput screening fingerprints} (HTSFPs), and an optional |
| 7434 | preloaded database that provides access to a substantial portion of publicly |
| 7435 | available bioactivity data.") |
| 7436 | (license license:artistic2.0))) |
| 7437 | |
| 7438 | (define-public r-biobroom |
| 7439 | (package |
| 7440 | (name "r-biobroom") |
| 7441 | (version "1.18.0") |
| 7442 | (source |
| 7443 | (origin |
| 7444 | (method url-fetch) |
| 7445 | (uri (bioconductor-uri "biobroom" version)) |
| 7446 | (sha256 |
| 7447 | (base32 |
| 7448 | "1480ycdsh9xdhbpr47vdw5g6m8arqsnp8hc19wwhzm8npxh4qqlb")))) |
| 7449 | (properties `((upstream-name . "biobroom"))) |
| 7450 | (build-system r-build-system) |
| 7451 | (propagated-inputs |
| 7452 | `(("r-biobase" ,r-biobase) |
| 7453 | ("r-broom" ,r-broom) |
| 7454 | ("r-dplyr" ,r-dplyr) |
| 7455 | ("r-tidyr" ,r-tidyr))) |
| 7456 | (home-page "https://github.com/StoreyLab/biobroom") |
| 7457 | (synopsis "Turn Bioconductor objects into tidy data frames") |
| 7458 | (description |
| 7459 | "This package contains methods for converting standard objects |
| 7460 | constructed by bioinformatics packages, especially those in Bioconductor, and |
| 7461 | converting them to @code{tidy} data. It thus serves as a complement to the |
| 7462 | @code{broom} package, and follows the same tidy, augment, glance division of |
| 7463 | tidying methods. Tidying data makes it easy to recombine, reshape and |
| 7464 | visualize bioinformatics analyses.") |
| 7465 | ;; Any version of the LGPL. |
| 7466 | (license license:lgpl3+))) |
| 7467 | |
| 7468 | (define-public r-graphite |
| 7469 | (package |
| 7470 | (name "r-graphite") |
| 7471 | (version "1.32.0") |
| 7472 | (source |
| 7473 | (origin |
| 7474 | (method url-fetch) |
| 7475 | (uri (bioconductor-uri "graphite" version)) |
| 7476 | (sha256 |
| 7477 | (base32 |
| 7478 | "1r9fk0cpdwm7012pa85dkjcpkml2j89zcznpf4hfdz66anfyyycd")))) |
| 7479 | (properties `((upstream-name . "graphite"))) |
| 7480 | (build-system r-build-system) |
| 7481 | (propagated-inputs |
| 7482 | `(("r-annotationdbi" ,r-annotationdbi) |
| 7483 | ("r-checkmate" ,r-checkmate) |
| 7484 | ("r-graph" ,r-graph) |
| 7485 | ("r-httr" ,r-httr) |
| 7486 | ("r-rappdirs" ,r-rappdirs))) |
| 7487 | (home-page "https://bioconductor.org/packages/graphite/") |
| 7488 | (synopsis "Networks from pathway databases") |
| 7489 | (description |
| 7490 | "Graphite provides networks derived from eight public pathway databases, |
| 7491 | and automates the conversion of node identifiers (e.g. from Entrez IDs to gene |
| 7492 | symbols).") |
| 7493 | (license license:agpl3+))) |
| 7494 | |
| 7495 | (define-public r-reactomepa |
| 7496 | (package |
| 7497 | (name "r-reactomepa") |
| 7498 | (version "1.30.0") |
| 7499 | (source |
| 7500 | (origin |
| 7501 | (method url-fetch) |
| 7502 | (uri (bioconductor-uri "ReactomePA" version)) |
| 7503 | (sha256 |
| 7504 | (base32 |
| 7505 | "1vwc9kj1l4yi7c4f4lnq0i3wl2nrmmhcxyakz8qak122fi92z3j1")))) |
| 7506 | (properties `((upstream-name . "ReactomePA"))) |
| 7507 | (build-system r-build-system) |
| 7508 | (propagated-inputs |
| 7509 | `(("r-annotationdbi" ,r-annotationdbi) |
| 7510 | ("r-dose" ,r-dose) |
| 7511 | ("r-enrichplot" ,r-enrichplot) |
| 7512 | ("r-ggplot2" ,r-ggplot2) |
| 7513 | ("r-ggraph" ,r-ggraph) |
| 7514 | ("r-graphite" ,r-graphite) |
| 7515 | ("r-igraph" ,r-igraph) |
| 7516 | ("r-reactome-db" ,r-reactome-db))) |
| 7517 | (home-page "https://guangchuangyu.github.io/software/ReactomePA") |
| 7518 | (synopsis "Reactome pathway analysis") |
| 7519 | (description |
| 7520 | "This package provides functions for pathway analysis based on the |
| 7521 | REACTOME pathway database. It implements enrichment analysis, gene set |
| 7522 | enrichment analysis and several functions for visualization.") |
| 7523 | (license license:gpl2))) |
| 7524 | |
| 7525 | (define-public r-ebarrays |
| 7526 | (package |
| 7527 | (name "r-ebarrays") |
| 7528 | (version "2.50.0") |
| 7529 | (source |
| 7530 | (origin |
| 7531 | (method url-fetch) |
| 7532 | (uri (bioconductor-uri "EBarrays" version)) |
| 7533 | (sha256 |
| 7534 | (base32 |
| 7535 | "063rhsdp8x0f881kslq06zxfp6b2qabrz4vmfrn8a4v3pd3n7s13")))) |
| 7536 | (properties `((upstream-name . "EBarrays"))) |
| 7537 | (build-system r-build-system) |
| 7538 | (propagated-inputs |
| 7539 | `(("r-biobase" ,r-biobase) |
| 7540 | ("r-cluster" ,r-cluster) |
| 7541 | ("r-lattice" ,r-lattice))) |
| 7542 | (home-page "https://bioconductor.org/packages/EBarrays/") |
| 7543 | (synopsis "Gene clustering and differential expression identification") |
| 7544 | (description |
| 7545 | "EBarrays provides tools for the analysis of replicated/unreplicated |
| 7546 | microarray data.") |
| 7547 | (license license:gpl2+))) |
| 7548 | |
| 7549 | (define-public r-bioccasestudies |
| 7550 | (package |
| 7551 | (name "r-bioccasestudies") |
| 7552 | (version "1.48.0") |
| 7553 | (source |
| 7554 | (origin |
| 7555 | (method url-fetch) |
| 7556 | (uri (bioconductor-uri "BiocCaseStudies" version)) |
| 7557 | (sha256 |
| 7558 | (base32 |
| 7559 | "1sg9vxs24zfz3dg9y0qlrdsq43y0pbahbvcfxzlxjzjw80xzxpbd")))) |
| 7560 | (properties |
| 7561 | `((upstream-name . "BiocCaseStudies"))) |
| 7562 | (build-system r-build-system) |
| 7563 | (propagated-inputs `(("r-biobase" ,r-biobase))) |
| 7564 | (home-page "https://bioconductor.org/packages/BiocCaseStudies") |
| 7565 | (synopsis "Support for the case studies monograph") |
| 7566 | (description |
| 7567 | "This package provides software and data to support the case studies |
| 7568 | monograph.") |
| 7569 | (license license:artistic2.0))) |
| 7570 | |
| 7571 | (define-public r-biocgraph |
| 7572 | (package |
| 7573 | (name "r-biocgraph") |
| 7574 | (version "1.48.0") |
| 7575 | (source |
| 7576 | (origin |
| 7577 | (method url-fetch) |
| 7578 | (uri (bioconductor-uri "biocGraph" version)) |
| 7579 | (sha256 |
| 7580 | (base32 |
| 7581 | "1rv2lwiqwg7h7za23n896fs4dpla3xhw6kzwghb6iw5nlm2m61yw")))) |
| 7582 | (properties `((upstream-name . "biocGraph"))) |
| 7583 | (build-system r-build-system) |
| 7584 | (propagated-inputs |
| 7585 | `(("r-biocgenerics" ,r-biocgenerics) |
| 7586 | ("r-geneplotter" ,r-geneplotter) |
| 7587 | ("r-graph" ,r-graph) |
| 7588 | ("r-rgraphviz" ,r-rgraphviz))) |
| 7589 | (home-page "https://bioconductor.org/packages/biocGraph/") |
| 7590 | (synopsis "Graph examples and use cases in Bioinformatics") |
| 7591 | (description |
| 7592 | "This package provides examples and code that make use of the |
| 7593 | different graph related packages produced by Bioconductor.") |
| 7594 | (license license:artistic2.0))) |
| 7595 | |
| 7596 | (define-public r-experimenthub |
| 7597 | (package |
| 7598 | (name "r-experimenthub") |
| 7599 | (version "1.12.0") |
| 7600 | (source |
| 7601 | (origin |
| 7602 | (method url-fetch) |
| 7603 | (uri (bioconductor-uri "ExperimentHub" version)) |
| 7604 | (sha256 |
| 7605 | (base32 |
| 7606 | "054w2lkyirbmhgia0rp4nk9zzw3zphz6jxg6fc9zlarp90g64z24")))) |
| 7607 | (properties `((upstream-name . "ExperimentHub"))) |
| 7608 | (build-system r-build-system) |
| 7609 | (propagated-inputs |
| 7610 | `(("r-annotationhub" ,r-annotationhub) |
| 7611 | ("r-biocfilecache" ,r-biocfilecache) |
| 7612 | ("r-biocgenerics" ,r-biocgenerics) |
| 7613 | ("r-biocmanager" ,r-biocmanager) |
| 7614 | ("r-curl" ,r-curl) |
| 7615 | ("r-rappdirs" ,r-rappdirs) |
| 7616 | ("r-s4vectors" ,r-s4vectors))) |
| 7617 | (home-page "https://bioconductor.org/packages/ExperimentHub/") |
| 7618 | (synopsis "Client to access ExperimentHub resources") |
| 7619 | (description |
| 7620 | "This package provides a client for the Bioconductor ExperimentHub web |
| 7621 | resource. ExperimentHub provides a central location where curated data from |
| 7622 | experiments, publications or training courses can be accessed. Each resource |
| 7623 | has associated metadata, tags and date of modification. The client creates |
| 7624 | and manages a local cache of files retrieved enabling quick and reproducible |
| 7625 | access.") |
| 7626 | (license license:artistic2.0))) |
| 7627 | |
| 7628 | (define-public r-multiassayexperiment |
| 7629 | (package |
| 7630 | (name "r-multiassayexperiment") |
| 7631 | (version "1.12.6") |
| 7632 | (source |
| 7633 | (origin |
| 7634 | (method url-fetch) |
| 7635 | (uri (bioconductor-uri "MultiAssayExperiment" version)) |
| 7636 | (sha256 |
| 7637 | (base32 |
| 7638 | "174vzlxsyayb5il77cb3zzgszxl3l0wkprc9w6pgz4yv5ix13adi")))) |
| 7639 | (properties |
| 7640 | `((upstream-name . "MultiAssayExperiment"))) |
| 7641 | (build-system r-build-system) |
| 7642 | (propagated-inputs |
| 7643 | `(("r-biobase" ,r-biobase) |
| 7644 | ("r-biocgenerics" ,r-biocgenerics) |
| 7645 | ("r-genomicranges" ,r-genomicranges) |
| 7646 | ("r-iranges" ,r-iranges) |
| 7647 | ("r-s4vectors" ,r-s4vectors) |
| 7648 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 7649 | ("r-tidyr" ,r-tidyr))) |
| 7650 | (native-inputs |
| 7651 | `(("r-knitr" ,r-knitr))) |
| 7652 | (home-page "https://waldronlab.io/MultiAssayExperiment/") |
| 7653 | (synopsis "Integration of multi-omics experiments in Bioconductor") |
| 7654 | (description |
| 7655 | "MultiAssayExperiment harmonizes data management of multiple assays |
| 7656 | performed on an overlapping set of specimens. It provides a familiar |
| 7657 | Bioconductor user experience by extending concepts from |
| 7658 | @code{SummarizedExperiment}, supporting an open-ended mix of standard data |
| 7659 | classes for individual assays, and allowing subsetting by genomic ranges or |
| 7660 | rownames.") |
| 7661 | (license license:artistic2.0))) |
| 7662 | |
| 7663 | (define-public r-bioconcotk |
| 7664 | (package |
| 7665 | (name "r-bioconcotk") |
| 7666 | (version "1.6.0") |
| 7667 | (source |
| 7668 | (origin |
| 7669 | (method url-fetch) |
| 7670 | (uri (bioconductor-uri "BiocOncoTK" version)) |
| 7671 | (sha256 |
| 7672 | (base32 |
| 7673 | "0rnah6c01a33yb9663jim9iclan61rpcwprb56mykgn1pf5hywbj")))) |
| 7674 | (properties `((upstream-name . "BiocOncoTK"))) |
| 7675 | (build-system r-build-system) |
| 7676 | (propagated-inputs |
| 7677 | `(("r-bigrquery" ,r-bigrquery) |
| 7678 | ("r-car" ,r-car) |
| 7679 | ("r-complexheatmap" ,r-complexheatmap) |
| 7680 | ("r-curatedtcgadata" ,r-curatedtcgadata) |
| 7681 | ("r-dbi" ,r-dbi) |
| 7682 | ("r-dplyr" ,r-dplyr) |
| 7683 | ("r-dt" ,r-dt) |
| 7684 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 7685 | ("r-genomicranges" ,r-genomicranges) |
| 7686 | ("r-ggplot2" ,r-ggplot2) |
| 7687 | ("r-ggpubr" ,r-ggpubr) |
| 7688 | ("r-graph" ,r-graph) |
| 7689 | ("r-httr" ,r-httr) |
| 7690 | ("r-iranges" ,r-iranges) |
| 7691 | ("r-magrittr" ,r-magrittr) |
| 7692 | ("r-plyr" ,r-plyr) |
| 7693 | ("r-rgraphviz" ,r-rgraphviz) |
| 7694 | ("r-rjson" ,r-rjson) |
| 7695 | ("r-s4vectors" ,r-s4vectors) |
| 7696 | ("r-scales" ,r-scales) |
| 7697 | ("r-shiny" ,r-shiny) |
| 7698 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 7699 | (home-page "https://bioconductor.org/packages/BiocOncoTK") |
| 7700 | (synopsis "Bioconductor components for general cancer genomics") |
| 7701 | (description |
| 7702 | "The purpose of this package is to provide a central interface to various |
| 7703 | tools for genome-scale analysis of cancer studies.") |
| 7704 | (license license:artistic2.0))) |
| 7705 | |
| 7706 | (define-public r-biocor |
| 7707 | (package |
| 7708 | (name "r-biocor") |
| 7709 | (version "1.10.0") |
| 7710 | (source |
| 7711 | (origin |
| 7712 | (method url-fetch) |
| 7713 | (uri (bioconductor-uri "BioCor" version)) |
| 7714 | (sha256 |
| 7715 | (base32 |
| 7716 | "1bjw02rwmz2d715sgpfp08njb15200ch7cmipsf9hd5835ppg1jl")))) |
| 7717 | (properties `((upstream-name . "BioCor"))) |
| 7718 | (build-system r-build-system) |
| 7719 | (propagated-inputs |
| 7720 | `(("r-biocparallel" ,r-biocparallel) |
| 7721 | ("r-gseabase" ,r-gseabase) |
| 7722 | ("r-matrix" ,r-matrix))) |
| 7723 | (home-page "https://llrs.github.io/BioCor/") |
| 7724 | (synopsis "Functional similarities") |
| 7725 | (description |
| 7726 | "This package provides tools to calculate functional similarities based |
| 7727 | on the pathways described on KEGG and REACTOME or in gene sets. These |
| 7728 | similarities can be calculated for pathways or gene sets, genes, or clusters |
| 7729 | and combined with other similarities. They can be used to improve networks, |
| 7730 | gene selection, testing relationships, and so on.") |
| 7731 | (license license:expat))) |
| 7732 | |
| 7733 | (define-public r-biocpkgtools |
| 7734 | (package |
| 7735 | (name "r-biocpkgtools") |
| 7736 | (version "1.4.6") |
| 7737 | (source |
| 7738 | (origin |
| 7739 | (method url-fetch) |
| 7740 | (uri (bioconductor-uri "BiocPkgTools" version)) |
| 7741 | (sha256 |
| 7742 | (base32 |
| 7743 | "0grwnmncmpqcplbfw3j210m1a8f7mmdizklh4zksg4ic21dpjj1a")))) |
| 7744 | (properties `((upstream-name . "BiocPkgTools"))) |
| 7745 | (build-system r-build-system) |
| 7746 | (propagated-inputs |
| 7747 | `(("r-biocfilecache" ,r-biocfilecache) |
| 7748 | ("r-biocmanager" ,r-biocmanager) |
| 7749 | ("r-biocviews" ,r-biocviews) |
| 7750 | ("r-dplyr" ,r-dplyr) |
| 7751 | ("r-dt" ,r-dt) |
| 7752 | ("r-gh" ,r-gh) |
| 7753 | ("r-graph" ,r-graph) |
| 7754 | ("r-htmltools" ,r-htmltools) |
| 7755 | ("r-htmlwidgets" ,r-htmlwidgets) |
| 7756 | ("r-httr" ,r-httr) |
| 7757 | ("r-igraph" ,r-igraph) |
| 7758 | ("r-jsonlite" ,r-jsonlite) |
| 7759 | ("r-magrittr" ,r-magrittr) |
| 7760 | ("r-rappdirs" ,r-rappdirs) |
| 7761 | ("r-rbgl" ,r-rbgl) |
| 7762 | ("r-readr" ,r-readr) |
| 7763 | ("r-rex" ,r-rex) |
| 7764 | ("r-rlang" ,r-rlang) |
| 7765 | ("r-rvest" ,r-rvest) |
| 7766 | ("r-stringr" ,r-stringr) |
| 7767 | ("r-tibble" ,r-tibble) |
| 7768 | ("r-tidyr" ,r-tidyr) |
| 7769 | ("r-tidyselect" ,r-tidyselect) |
| 7770 | ("r-xml2" ,r-xml2))) |
| 7771 | (native-inputs |
| 7772 | `(("r-knitr" ,r-knitr))) |
| 7773 | (home-page "https://github.com/seandavi/BiocPkgTools") |
| 7774 | (synopsis "Collection of tools for learning about Bioconductor packages") |
| 7775 | (description |
| 7776 | "Bioconductor has a rich ecosystem of metadata around packages, usage, |
| 7777 | and build status. This package is a simple collection of functions to access |
| 7778 | that metadata from R. The goal is to expose metadata for data mining and |
| 7779 | value-added functionality such as package searching, text mining, and |
| 7780 | analytics on packages.") |
| 7781 | (license license:expat))) |
| 7782 | |
| 7783 | (define-public r-biocset |
| 7784 | (package |
| 7785 | (name "r-biocset") |
| 7786 | (version "1.0.1") |
| 7787 | (source |
| 7788 | (origin |
| 7789 | (method url-fetch) |
| 7790 | (uri (bioconductor-uri "BiocSet" version)) |
| 7791 | (sha256 |
| 7792 | (base32 |
| 7793 | "1xcksnvjflrdarn8xqmgf0n6wbsjkq9jazqwp35i52vqcq4ic1j9")))) |
| 7794 | (properties `((upstream-name . "BiocSet"))) |
| 7795 | (build-system r-build-system) |
| 7796 | (propagated-inputs |
| 7797 | `(("r-annotationdbi" ,r-annotationdbi) |
| 7798 | ("r-dplyr" ,r-dplyr) |
| 7799 | ("r-keggrest" ,r-keggrest) |
| 7800 | ("r-plyr" ,r-plyr) |
| 7801 | ("r-rlang" ,r-rlang) |
| 7802 | ("r-rtracklayer" ,r-rtracklayer) |
| 7803 | ("r-tibble" ,r-tibble))) |
| 7804 | (home-page |
| 7805 | "https://bioconductor.org/packages/BiocSet") |
| 7806 | (synopsis |
| 7807 | "Representing Different Biological Sets") |
| 7808 | (description |
| 7809 | "BiocSet displays different biological sets in a triple tibble format. |
| 7810 | These three tibbles are @code{element}, @code{set}, and @code{elementset}. |
| 7811 | The user has the ability to activate one of these three tibbles to perform |
| 7812 | common functions from the @code{dplyr} package. Mapping functionality and |
| 7813 | accessing web references for elements/sets are also available in BiocSet.") |
| 7814 | (license license:artistic2.0))) |
| 7815 | |
| 7816 | (define-public r-biocworkflowtools |
| 7817 | (package |
| 7818 | (name "r-biocworkflowtools") |
| 7819 | (version "1.12.1") |
| 7820 | (source |
| 7821 | (origin |
| 7822 | (method url-fetch) |
| 7823 | (uri (bioconductor-uri "BiocWorkflowTools" version)) |
| 7824 | (sha256 |
| 7825 | (base32 |
| 7826 | "0z28s572wg9qxv52dmixxz1xf1z3fyp2j7kzk0k32fp628918wr6")))) |
| 7827 | (properties |
| 7828 | `((upstream-name . "BiocWorkflowTools"))) |
| 7829 | (build-system r-build-system) |
| 7830 | (propagated-inputs |
| 7831 | `(("r-biocstyle" ,r-biocstyle) |
| 7832 | ("r-bookdown" ,r-bookdown) |
| 7833 | ("r-git2r" ,r-git2r) |
| 7834 | ("r-httr" ,r-httr) |
| 7835 | ("r-knitr" ,r-knitr) |
| 7836 | ("r-rmarkdown" ,r-rmarkdown) |
| 7837 | ("r-rstudioapi" ,r-rstudioapi) |
| 7838 | ("r-stringr" ,r-stringr) |
| 7839 | ("r-usethis" ,r-usethis))) |
| 7840 | (native-inputs |
| 7841 | `(("r-knitr" ,r-knitr))) |
| 7842 | (home-page "https://bioconductor.org/packages/BiocWorkflowTools/") |
| 7843 | (synopsis "Tools to aid the development of Bioconductor Workflow packages") |
| 7844 | (description |
| 7845 | "This package provides functions to ease the transition between |
| 7846 | Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.") |
| 7847 | (license license:expat))) |
| 7848 | |
| 7849 | (define-public r-biodist |
| 7850 | (package |
| 7851 | (name "r-biodist") |
| 7852 | (version "1.58.0") |
| 7853 | (source |
| 7854 | (origin |
| 7855 | (method url-fetch) |
| 7856 | (uri (bioconductor-uri "bioDist" version)) |
| 7857 | (sha256 |
| 7858 | (base32 |
| 7859 | "0iabw07px3ybdgbbab0vv350051cm4aq8w47rz9dnmzx4kil9h5q")))) |
| 7860 | (properties `((upstream-name . "bioDist"))) |
| 7861 | (build-system r-build-system) |
| 7862 | (propagated-inputs |
| 7863 | `(("r-biobase" ,r-biobase) |
| 7864 | ("r-kernsmooth" ,r-kernsmooth))) |
| 7865 | (home-page "https://bioconductor.org/packages/bioDist/") |
| 7866 | (synopsis "Different distance measures") |
| 7867 | (description |
| 7868 | "This package provides a collection of software tools for calculating |
| 7869 | distance measures.") |
| 7870 | (license license:artistic2.0))) |