| 1 | ;;; GNU Guix --- Functional package management for GNU |
| 2 | ;;; Copyright © 2016, 2017, 2018, 2019 Ricardo Wurmus <rekado@elephly.net> |
| 3 | ;;; Copyright © 2016, 2017, 2018 Roel Janssen <roel@gnu.org> |
| 4 | ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> |
| 5 | ;;; |
| 6 | ;;; This file is part of GNU Guix. |
| 7 | ;;; |
| 8 | ;;; GNU Guix is free software; you can redistribute it and/or modify it |
| 9 | ;;; under the terms of the GNU General Public License as published by |
| 10 | ;;; the Free Software Foundation; either version 3 of the License, or (at |
| 11 | ;;; your option) any later version. |
| 12 | ;;; |
| 13 | ;;; GNU Guix is distributed in the hope that it will be useful, but |
| 14 | ;;; WITHOUT ANY WARRANTY; without even the implied warranty of |
| 15 | ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
| 16 | ;;; GNU General Public License for more details. |
| 17 | ;;; |
| 18 | ;;; You should have received a copy of the GNU General Public License |
| 19 | ;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>. |
| 20 | |
| 21 | (define-module (gnu packages bioconductor) |
| 22 | #:use-module ((guix licenses) #:prefix license:) |
| 23 | #:use-module (guix packages) |
| 24 | #:use-module (guix download) |
| 25 | #:use-module (guix build-system r) |
| 26 | #:use-module (gnu packages) |
| 27 | #:use-module (gnu packages bioinformatics) |
| 28 | #:use-module (gnu packages cran) |
| 29 | #:use-module (gnu packages compression) |
| 30 | #:use-module (gnu packages gcc) |
| 31 | #:use-module (gnu packages graph) |
| 32 | #:use-module (gnu packages haskell) |
| 33 | #:use-module (gnu packages image) |
| 34 | #:use-module (gnu packages maths) |
| 35 | #:use-module (gnu packages netpbm) |
| 36 | #:use-module (gnu packages perl) |
| 37 | #:use-module (gnu packages pkg-config) |
| 38 | #:use-module (gnu packages statistics) |
| 39 | #:use-module (gnu packages web)) |
| 40 | |
| 41 | \f |
| 42 | ;;; Annotations |
| 43 | |
| 44 | (define-public r-bsgenome-celegans-ucsc-ce6 |
| 45 | (package |
| 46 | (name "r-bsgenome-celegans-ucsc-ce6") |
| 47 | (version "1.4.0") |
| 48 | (source (origin |
| 49 | (method url-fetch) |
| 50 | ;; We cannot use bioconductor-uri here because this tarball is |
| 51 | ;; located under "data/annotation/" instead of "bioc/". |
| 52 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 53 | "release/data/annotation/src/contrib/" |
| 54 | "BSgenome.Celegans.UCSC.ce6_" |
| 55 | version ".tar.gz")) |
| 56 | (sha256 |
| 57 | (base32 |
| 58 | "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) |
| 59 | (properties |
| 60 | `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) |
| 61 | (build-system r-build-system) |
| 62 | ;; As this package provides little more than a very large data file it |
| 63 | ;; doesn't make sense to build substitutes. |
| 64 | (arguments `(#:substitutable? #f)) |
| 65 | (propagated-inputs |
| 66 | `(("r-bsgenome" ,r-bsgenome))) |
| 67 | (home-page |
| 68 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/") |
| 69 | (synopsis "Full genome sequences for Worm") |
| 70 | (description |
| 71 | "This package provides full genome sequences for Caenorhabditis |
| 72 | elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings |
| 73 | objects.") |
| 74 | (license license:artistic2.0))) |
| 75 | |
| 76 | (define-public r-bsgenome-celegans-ucsc-ce10 |
| 77 | (package |
| 78 | (name "r-bsgenome-celegans-ucsc-ce10") |
| 79 | (version "1.4.0") |
| 80 | (source (origin |
| 81 | (method url-fetch) |
| 82 | ;; We cannot use bioconductor-uri here because this tarball is |
| 83 | ;; located under "data/annotation/" instead of "bioc/". |
| 84 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 85 | "release/data/annotation/src/contrib/" |
| 86 | "BSgenome.Celegans.UCSC.ce10_" |
| 87 | version ".tar.gz")) |
| 88 | (sha256 |
| 89 | (base32 |
| 90 | "1zaym97jk4npxk14ifvwz2rvhm4zx9xgs33r9vvx9rlynp0gydrk")))) |
| 91 | (properties |
| 92 | `((upstream-name . "BSgenome.Celegans.UCSC.ce10"))) |
| 93 | (build-system r-build-system) |
| 94 | ;; As this package provides little more than a very large data file it |
| 95 | ;; doesn't make sense to build substitutes. |
| 96 | (arguments `(#:substitutable? #f)) |
| 97 | (propagated-inputs |
| 98 | `(("r-bsgenome" ,r-bsgenome))) |
| 99 | (home-page |
| 100 | "https://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce10/") |
| 101 | (synopsis "Full genome sequences for Worm") |
| 102 | (description |
| 103 | "This package provides full genome sequences for Caenorhabditis |
| 104 | elegans (Worm) as provided by UCSC (ce10, Oct 2010) and stored in Biostrings |
| 105 | objects.") |
| 106 | (license license:artistic2.0))) |
| 107 | |
| 108 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
| 109 | (package |
| 110 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") |
| 111 | (version "1.4.1") |
| 112 | (source (origin |
| 113 | (method url-fetch) |
| 114 | ;; We cannot use bioconductor-uri here because this tarball is |
| 115 | ;; located under "data/annotation/" instead of "bioc/". |
| 116 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 117 | "release/data/annotation/src/contrib/" |
| 118 | "BSgenome.Dmelanogaster.UCSC.dm6_" |
| 119 | version ".tar.gz")) |
| 120 | (sha256 |
| 121 | (base32 |
| 122 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) |
| 123 | (properties |
| 124 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) |
| 125 | (build-system r-build-system) |
| 126 | ;; As this package provides little more than a very large data file it |
| 127 | ;; doesn't make sense to build substitutes. |
| 128 | (arguments `(#:substitutable? #f)) |
| 129 | (propagated-inputs |
| 130 | `(("r-bsgenome" ,r-bsgenome))) |
| 131 | (home-page |
| 132 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") |
| 133 | (synopsis "Full genome sequences for Fly") |
| 134 | (description |
| 135 | "This package provides full genome sequences for Drosophila |
| 136 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings |
| 137 | objects.") |
| 138 | (license license:artistic2.0))) |
| 139 | |
| 140 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3 |
| 141 | (package |
| 142 | (name "r-bsgenome-dmelanogaster-ucsc-dm3") |
| 143 | (version "1.4.0") |
| 144 | (source (origin |
| 145 | (method url-fetch) |
| 146 | ;; We cannot use bioconductor-uri here because this tarball is |
| 147 | ;; located under "data/annotation/" instead of "bioc/". |
| 148 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 149 | "release/data/annotation/src/contrib/" |
| 150 | "BSgenome.Dmelanogaster.UCSC.dm3_" |
| 151 | version ".tar.gz")) |
| 152 | (sha256 |
| 153 | (base32 |
| 154 | "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) |
| 155 | (properties |
| 156 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) |
| 157 | (build-system r-build-system) |
| 158 | ;; As this package provides little more than a very large data file it |
| 159 | ;; doesn't make sense to build substitutes. |
| 160 | (arguments `(#:substitutable? #f)) |
| 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 | ;; We cannot use bioconductor-uri here because this tarball is |
| 179 | ;; located under "data/annotation/" instead of "bioc/". |
| 180 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 181 | "release/data/annotation/src/contrib/" |
| 182 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" |
| 183 | version ".tar.gz")) |
| 184 | (sha256 |
| 185 | (base32 |
| 186 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) |
| 187 | (properties |
| 188 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) |
| 189 | (build-system r-build-system) |
| 190 | (propagated-inputs |
| 191 | `(("r-bsgenome" ,r-bsgenome) |
| 192 | ("r-bsgenome-dmelanogaster-ucsc-dm3" |
| 193 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) |
| 194 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") |
| 195 | (synopsis "Full masked genome sequences for Fly") |
| 196 | (description |
| 197 | "This package provides full masked genome sequences for Drosophila |
| 198 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in |
| 199 | Biostrings objects. The sequences are the same as in |
| 200 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following |
| 201 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of |
| 202 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from |
| 203 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats |
| 204 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") |
| 205 | (license license:artistic2.0))) |
| 206 | |
| 207 | (define-public r-bsgenome-hsapiens-1000genomes-hs37d5 |
| 208 | (package |
| 209 | (name "r-bsgenome-hsapiens-1000genomes-hs37d5") |
| 210 | (version "0.99.1") |
| 211 | (source (origin |
| 212 | (method url-fetch) |
| 213 | ;; We cannot use bioconductor-uri here because this tarball is |
| 214 | ;; located under "data/annotation/" instead of "bioc/". |
| 215 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 216 | "release/data/annotation/src/contrib/" |
| 217 | "BSgenome.Hsapiens.1000genomes.hs37d5_" |
| 218 | version ".tar.gz")) |
| 219 | (sha256 |
| 220 | (base32 |
| 221 | "1cg0g5fqmsvwyw2p9hp2yy4ilk21jkbbrnpgqvb5c36ihjwvc7sr")))) |
| 222 | (properties |
| 223 | `((upstream-name . "BSgenome.Hsapiens.1000genomes.hs37d5"))) |
| 224 | (build-system r-build-system) |
| 225 | ;; As this package provides little more than a very large data file it |
| 226 | ;; doesn't make sense to build substitutes. |
| 227 | (arguments `(#:substitutable? #f)) |
| 228 | (propagated-inputs |
| 229 | `(("r-bsgenome" ,r-bsgenome))) |
| 230 | (home-page |
| 231 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.1000genomes.hs37d5/") |
| 232 | (synopsis "Full genome sequences for Homo sapiens") |
| 233 | (description |
| 234 | "This package provides full genome sequences for Homo sapiens from |
| 235 | 1000genomes phase2 reference genome sequence (hs37d5), based on NCBI GRCh37.") |
| 236 | (license license:artistic2.0))) |
| 237 | |
| 238 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
| 239 | (package |
| 240 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") |
| 241 | (version "1.3.99") |
| 242 | (source (origin |
| 243 | (method url-fetch) |
| 244 | ;; We cannot use bioconductor-uri here because this tarball is |
| 245 | ;; located under "data/annotation/" instead of "bioc/". |
| 246 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 247 | "release/data/annotation/src/contrib/" |
| 248 | "BSgenome.Hsapiens.UCSC.hg19.masked_" |
| 249 | version ".tar.gz")) |
| 250 | (sha256 |
| 251 | (base32 |
| 252 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) |
| 253 | (properties |
| 254 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) |
| 255 | (build-system r-build-system) |
| 256 | (propagated-inputs |
| 257 | `(("r-bsgenome" ,r-bsgenome) |
| 258 | ("r-bsgenome-hsapiens-ucsc-hg19" |
| 259 | ,r-bsgenome-hsapiens-ucsc-hg19))) |
| 260 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") |
| 261 | (synopsis "Full masked genome sequences for Homo sapiens") |
| 262 | (description |
| 263 | "This package provides full genome sequences for Homo sapiens (Human) as |
| 264 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The |
| 265 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of |
| 266 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS |
| 267 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of |
| 268 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem |
| 269 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by |
| 270 | default.") |
| 271 | (license license:artistic2.0))) |
| 272 | |
| 273 | (define-public r-bsgenome-mmusculus-ucsc-mm9 |
| 274 | (package |
| 275 | (name "r-bsgenome-mmusculus-ucsc-mm9") |
| 276 | (version "1.4.0") |
| 277 | (source (origin |
| 278 | (method url-fetch) |
| 279 | ;; We cannot use bioconductor-uri here because this tarball is |
| 280 | ;; located under "data/annotation/" instead of "bioc/". |
| 281 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 282 | "release/data/annotation/src/contrib/" |
| 283 | "BSgenome.Mmusculus.UCSC.mm9_" |
| 284 | version ".tar.gz")) |
| 285 | (sha256 |
| 286 | (base32 |
| 287 | "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) |
| 288 | (properties |
| 289 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) |
| 290 | (build-system r-build-system) |
| 291 | ;; As this package provides little more than a very large data file it |
| 292 | ;; doesn't make sense to build substitutes. |
| 293 | (arguments `(#:substitutable? #f)) |
| 294 | (propagated-inputs |
| 295 | `(("r-bsgenome" ,r-bsgenome))) |
| 296 | (home-page |
| 297 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/") |
| 298 | (synopsis "Full genome sequences for Mouse") |
| 299 | (description |
| 300 | "This package provides full genome sequences for Mus musculus (Mouse) as |
| 301 | provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") |
| 302 | (license license:artistic2.0))) |
| 303 | |
| 304 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
| 305 | (package |
| 306 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") |
| 307 | (version "1.3.99") |
| 308 | (source (origin |
| 309 | (method url-fetch) |
| 310 | ;; We cannot use bioconductor-uri here because this tarball is |
| 311 | ;; located under "data/annotation/" instead of "bioc/". |
| 312 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 313 | "release/data/annotation/src/contrib/" |
| 314 | "BSgenome.Mmusculus.UCSC.mm9.masked_" |
| 315 | version ".tar.gz")) |
| 316 | (sha256 |
| 317 | (base32 |
| 318 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) |
| 319 | (properties |
| 320 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) |
| 321 | (build-system r-build-system) |
| 322 | (propagated-inputs |
| 323 | `(("r-bsgenome" ,r-bsgenome) |
| 324 | ("r-bsgenome-mmusculus-ucsc-mm9" |
| 325 | ,r-bsgenome-mmusculus-ucsc-mm9))) |
| 326 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") |
| 327 | (synopsis "Full masked genome sequences for Mouse") |
| 328 | (description |
| 329 | "This package provides full genome sequences for Mus musculus (Mouse) as |
| 330 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The |
| 331 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of |
| 332 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS |
| 333 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of |
| 334 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem |
| 335 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by |
| 336 | default." ) |
| 337 | (license license:artistic2.0))) |
| 338 | |
| 339 | (define-public r-bsgenome-mmusculus-ucsc-mm10 |
| 340 | (package |
| 341 | (name "r-bsgenome-mmusculus-ucsc-mm10") |
| 342 | (version "1.4.0") |
| 343 | (source (origin |
| 344 | (method url-fetch) |
| 345 | ;; We cannot use bioconductor-uri here because this tarball is |
| 346 | ;; located under "data/annotation/" instead of "bioc/". |
| 347 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 348 | "release/data/annotation/src/contrib/" |
| 349 | "BSgenome.Mmusculus.UCSC.mm10_" |
| 350 | version ".tar.gz")) |
| 351 | (sha256 |
| 352 | (base32 |
| 353 | "12s0nm2na9brjad4rn9l7d3db2aj8qa1xvz0y1k7gk08wayb6bkf")))) |
| 354 | (properties |
| 355 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm10"))) |
| 356 | (build-system r-build-system) |
| 357 | ;; As this package provides little more than a very large data file it |
| 358 | ;; doesn't make sense to build substitutes. |
| 359 | (arguments `(#:substitutable? #f)) |
| 360 | (propagated-inputs |
| 361 | `(("r-bsgenome" ,r-bsgenome))) |
| 362 | (home-page |
| 363 | "https://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm10/") |
| 364 | (synopsis "Full genome sequences for Mouse") |
| 365 | (description |
| 366 | "This package provides full genome sequences for Mus |
| 367 | musculus (Mouse) as provided by UCSC (mm10, December 2011) and stored |
| 368 | in Biostrings objects.") |
| 369 | (license license:artistic2.0))) |
| 370 | |
| 371 | (define-public r-org-ce-eg-db |
| 372 | (package |
| 373 | (name "r-org-ce-eg-db") |
| 374 | (version "3.7.0") |
| 375 | (source (origin |
| 376 | (method url-fetch) |
| 377 | ;; We cannot use bioconductor-uri here because this tarball is |
| 378 | ;; located under "data/annotation/" instead of "bioc/". |
| 379 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 380 | "release/data/annotation/src/contrib/" |
| 381 | "org.Ce.eg.db_" version ".tar.gz")) |
| 382 | (sha256 |
| 383 | (base32 |
| 384 | "1w5br1ss4ha8wv4v2saj7cmbjc2jw0dyj2f2y269l078z31wcnaz")))) |
| 385 | (properties |
| 386 | `((upstream-name . "org.Ce.eg.db"))) |
| 387 | (build-system r-build-system) |
| 388 | (propagated-inputs |
| 389 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 390 | (home-page "https://www.bioconductor.org/packages/org.Ce.eg.db/") |
| 391 | (synopsis "Genome wide annotation for Worm") |
| 392 | (description |
| 393 | "This package provides mappings from Entrez gene identifiers to various |
| 394 | annotations for the genome of the model worm Caenorhabditis elegans.") |
| 395 | (license license:artistic2.0))) |
| 396 | |
| 397 | (define-public r-org-dm-eg-db |
| 398 | (package |
| 399 | (name "r-org-dm-eg-db") |
| 400 | (version "3.7.0") |
| 401 | (source (origin |
| 402 | (method url-fetch) |
| 403 | ;; We cannot use bioconductor-uri here because this tarball is |
| 404 | ;; located under "data/annotation/" instead of "bioc/". |
| 405 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 406 | "release/data/annotation/src/contrib/" |
| 407 | "org.Dm.eg.db_" version ".tar.gz")) |
| 408 | (sha256 |
| 409 | (base32 |
| 410 | "1pqjrzlyg72bjpy8zsxvaglc7jsv176bnyi87xdajmkvsgxpm7b3")))) |
| 411 | (properties |
| 412 | `((upstream-name . "org.Dm.eg.db"))) |
| 413 | (build-system r-build-system) |
| 414 | (propagated-inputs |
| 415 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 416 | (home-page "https://www.bioconductor.org/packages/org.Dm.eg.db/") |
| 417 | (synopsis "Genome wide annotation for Fly") |
| 418 | (description |
| 419 | "This package provides mappings from Entrez gene identifiers to various |
| 420 | annotations for the genome of the model fruit fly Drosophila melanogaster.") |
| 421 | (license license:artistic2.0))) |
| 422 | |
| 423 | (define-public r-org-dr-eg-db |
| 424 | (package |
| 425 | (name "r-org-dr-eg-db") |
| 426 | (version "3.7.0") |
| 427 | (source (origin |
| 428 | (method url-fetch) |
| 429 | ;; We cannot use bioconductor-uri here because this tarball is |
| 430 | ;; located under "data/annotation/" instead of "bioc/". |
| 431 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 432 | "release/data/annotation/src/contrib/" |
| 433 | "org.Dr.eg.db_" version ".tar.gz")) |
| 434 | (sha256 |
| 435 | (base32 |
| 436 | "1xs5wsbcpy0iwbjyiv7fax57djqc529ai5fk1qfsdcvlja3cpglx")))) |
| 437 | (properties |
| 438 | `((upstream-name . "org.Dr.eg.db"))) |
| 439 | (build-system r-build-system) |
| 440 | (propagated-inputs |
| 441 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 442 | (home-page "https://www.bioconductor.org/packages/org.Dr.eg.db/") |
| 443 | (synopsis "Annotation for Zebrafish") |
| 444 | (description |
| 445 | "This package provides genome wide annotations for Zebrafish, primarily |
| 446 | based on mapping using Entrez Gene identifiers.") |
| 447 | (license license:artistic2.0))) |
| 448 | |
| 449 | (define-public r-org-hs-eg-db |
| 450 | (package |
| 451 | (name "r-org-hs-eg-db") |
| 452 | (version "3.7.0") |
| 453 | (source (origin |
| 454 | (method url-fetch) |
| 455 | ;; We cannot use bioconductor-uri here because this tarball is |
| 456 | ;; located under "data/annotation/" instead of "bioc/". |
| 457 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 458 | "release/data/annotation/src/contrib/" |
| 459 | "org.Hs.eg.db_" version ".tar.gz")) |
| 460 | (sha256 |
| 461 | (base32 |
| 462 | "1qxz9l80yg3qdqszs6dsscp7lrpfi1bgd0pxh9j7q34vprzwhdim")))) |
| 463 | (properties |
| 464 | `((upstream-name . "org.Hs.eg.db"))) |
| 465 | (build-system r-build-system) |
| 466 | (propagated-inputs |
| 467 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 468 | (home-page "https://www.bioconductor.org/packages/org.Hs.eg.db/") |
| 469 | (synopsis "Genome wide annotation for Human") |
| 470 | (description |
| 471 | "This package contains genome-wide annotations for Human, primarily based |
| 472 | on mapping using Entrez Gene identifiers.") |
| 473 | (license license:artistic2.0))) |
| 474 | |
| 475 | (define-public r-org-mm-eg-db |
| 476 | (package |
| 477 | (name "r-org-mm-eg-db") |
| 478 | (version "3.7.0") |
| 479 | (source (origin |
| 480 | (method url-fetch) |
| 481 | ;; We cannot use bioconductor-uri here because this tarball is |
| 482 | ;; located under "data/annotation/" instead of "bioc/". |
| 483 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 484 | "release/data/annotation/src/contrib/" |
| 485 | "org.Mm.eg.db_" version ".tar.gz")) |
| 486 | (sha256 |
| 487 | (base32 |
| 488 | "1i3nvrd3wjigf1rmgxq1p5xxc3p8v02h5gwi62s30rkrsyjjfjxx")))) |
| 489 | (properties |
| 490 | `((upstream-name . "org.Mm.eg.db"))) |
| 491 | (build-system r-build-system) |
| 492 | (propagated-inputs |
| 493 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 494 | (home-page "https://www.bioconductor.org/packages/org.Mm.eg.db/") |
| 495 | (synopsis "Genome wide annotation for Mouse") |
| 496 | (description |
| 497 | "This package provides mappings from Entrez gene identifiers to various |
| 498 | annotations for the genome of the model mouse Mus musculus.") |
| 499 | (license license:artistic2.0))) |
| 500 | |
| 501 | (define-public r-bsgenome-hsapiens-ucsc-hg19 |
| 502 | (package |
| 503 | (name "r-bsgenome-hsapiens-ucsc-hg19") |
| 504 | (version "1.4.0") |
| 505 | (source (origin |
| 506 | (method url-fetch) |
| 507 | ;; We cannot use bioconductor-uri here because this tarball is |
| 508 | ;; located under "data/annotation/" instead of "bioc/". |
| 509 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 510 | "release/data/annotation/src/contrib/" |
| 511 | "BSgenome.Hsapiens.UCSC.hg19_" |
| 512 | version ".tar.gz")) |
| 513 | (sha256 |
| 514 | (base32 |
| 515 | "1y0nqpk8cw5a34sd9hmin3z4v7iqm6hf6l22cl81vlbxqbjibxc8")))) |
| 516 | (properties |
| 517 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19"))) |
| 518 | (build-system r-build-system) |
| 519 | ;; As this package provides little more than a very large data file it |
| 520 | ;; doesn't make sense to build substitutes. |
| 521 | (arguments `(#:substitutable? #f)) |
| 522 | (propagated-inputs |
| 523 | `(("r-bsgenome" ,r-bsgenome))) |
| 524 | (home-page |
| 525 | "https://www.bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19/") |
| 526 | (synopsis "Full genome sequences for Homo sapiens") |
| 527 | (description |
| 528 | "This package provides full genome sequences for Homo sapiens as provided |
| 529 | by UCSC (hg19, February 2009) and stored in Biostrings objects.") |
| 530 | (license license:artistic2.0))) |
| 531 | |
| 532 | (define-public r-genelendatabase |
| 533 | (package |
| 534 | (name "r-genelendatabase") |
| 535 | (version "1.18.0") |
| 536 | (source |
| 537 | (origin |
| 538 | (method url-fetch) |
| 539 | ;; We cannot use bioconductor-uri here because this tarball is |
| 540 | ;; located under "data/experiment/" instead of "bioc/". |
| 541 | (uri (string-append "https://bioconductor.org/packages/" |
| 542 | "release/data/experiment/src/contrib" |
| 543 | "/geneLenDataBase_" version ".tar.gz")) |
| 544 | (sha256 |
| 545 | (base32 |
| 546 | "03gm4pvsfascx7kjg0jycpf4f572mja68wwmwigs390vbmawyb4a")))) |
| 547 | (properties |
| 548 | `((upstream-name . "geneLenDataBase"))) |
| 549 | (build-system r-build-system) |
| 550 | (propagated-inputs |
| 551 | `(("r-rtracklayer" ,r-rtracklayer) |
| 552 | ("r-genomicfeatures" ,r-genomicfeatures))) |
| 553 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") |
| 554 | (synopsis "Lengths of mRNA transcripts for a number of genomes") |
| 555 | (description |
| 556 | "This package provides the lengths of mRNA transcripts for a number of |
| 557 | genomes and gene ID formats, largely based on the UCSC table browser.") |
| 558 | (license license:lgpl2.0+))) |
| 559 | |
| 560 | (define-public r-txdb-hsapiens-ucsc-hg19-knowngene |
| 561 | (package |
| 562 | (name "r-txdb-hsapiens-ucsc-hg19-knowngene") |
| 563 | (version "3.2.2") |
| 564 | (source (origin |
| 565 | (method url-fetch) |
| 566 | ;; We cannot use bioconductor-uri here because this tarball is |
| 567 | ;; located under "data/annotation/" instead of "bioc/". |
| 568 | (uri (string-append "https://bioconductor.org/packages/" |
| 569 | "release/data/annotation/src/contrib" |
| 570 | "/TxDb.Hsapiens.UCSC.hg19.knownGene_" |
| 571 | version ".tar.gz")) |
| 572 | (sha256 |
| 573 | (base32 |
| 574 | "1sajhcqqwazgz2lqbik7rd935i7kpnh08zxbp2ra10j72yqy4g86")))) |
| 575 | (properties |
| 576 | `((upstream-name . "TxDb.Hsapiens.UCSC.hg19.knownGene"))) |
| 577 | (build-system r-build-system) |
| 578 | ;; As this package provides little more than a very large data file it |
| 579 | ;; doesn't make sense to build substitutes. |
| 580 | (arguments `(#:substitutable? #f)) |
| 581 | (propagated-inputs |
| 582 | `(("r-genomicfeatures" ,r-genomicfeatures))) |
| 583 | (home-page |
| 584 | "https://bioconductor.org/packages/TxDb.Hsapiens.UCSC.hg19.knownGene/") |
| 585 | (synopsis "Annotation package for human genome in TxDb format") |
| 586 | (description |
| 587 | "This package provides an annotation database of Homo sapiens genome |
| 588 | data. It is derived from the UCSC hg19 genome and based on the \"knownGene\" |
| 589 | track. The database is exposed as a @code{TxDb} object.") |
| 590 | (license license:artistic2.0))) |
| 591 | |
| 592 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
| 593 | (package |
| 594 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") |
| 595 | (version "3.2.2") |
| 596 | (source (origin |
| 597 | (method url-fetch) |
| 598 | ;; We cannot use bioconductor-uri here because this tarball is |
| 599 | ;; located under "data/annotation/" instead of "bioc/". |
| 600 | (uri (string-append "https://bioconductor.org/packages/" |
| 601 | "release/data/annotation/src/contrib" |
| 602 | "/TxDb.Mmusculus.UCSC.mm9.knownGene_" |
| 603 | version ".tar.gz")) |
| 604 | (sha256 |
| 605 | (base32 |
| 606 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) |
| 607 | (properties |
| 608 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) |
| 609 | (build-system r-build-system) |
| 610 | (propagated-inputs |
| 611 | `(("r-genomicfeatures" ,r-genomicfeatures) |
| 612 | ("r-annotationdbi" ,r-annotationdbi))) |
| 613 | (home-page |
| 614 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") |
| 615 | (synopsis "Annotation package for mouse genome in TxDb format") |
| 616 | (description |
| 617 | "This package provides an annotation database of Mouse genome data. It |
| 618 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The |
| 619 | database is exposed as a @code{TxDb} object.") |
| 620 | (license license:artistic2.0))) |
| 621 | |
| 622 | (define-public r-txdb-mmusculus-ucsc-mm10-knowngene |
| 623 | (package |
| 624 | (name "r-txdb-mmusculus-ucsc-mm10-knowngene") |
| 625 | (version "3.4.4") |
| 626 | (source (origin |
| 627 | (method url-fetch) |
| 628 | ;; We cannot use bioconductor-uri here because this tarball is |
| 629 | ;; located under "data/annotation/" instead of "bioc/". |
| 630 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 631 | "release/data/annotation/src/contrib/" |
| 632 | "TxDb.Mmusculus.UCSC.mm10.knownGene_" |
| 633 | version ".tar.gz")) |
| 634 | (sha256 |
| 635 | (base32 |
| 636 | "01lgxc1fx5nhlpbwjd5zqghkkbmh6axd98ikx4b0spv0jdg6gf39")))) |
| 637 | (properties |
| 638 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm10.knownGene"))) |
| 639 | (build-system r-build-system) |
| 640 | ;; As this package provides little more than a very large data file it |
| 641 | ;; doesn't make sense to build substitutes. |
| 642 | (arguments `(#:substitutable? #f)) |
| 643 | (propagated-inputs |
| 644 | `(("r-bsgenome" ,r-bsgenome) |
| 645 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 646 | ("r-annotationdbi" ,r-annotationdbi))) |
| 647 | (home-page |
| 648 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm10.knownGene/") |
| 649 | (synopsis "Annotation package for TxDb knownGene object(s) for Mouse") |
| 650 | (description |
| 651 | "This package loads a TxDb object, which is an R interface to |
| 652 | prefabricated databases contained in this package. This package provides |
| 653 | the TxDb object of Mouse data as provided by UCSC (mm10, December 2011) |
| 654 | based on the knownGene track.") |
| 655 | (license license:artistic2.0))) |
| 656 | |
| 657 | (define-public r-fdb-infiniummethylation-hg19 |
| 658 | (package |
| 659 | (name "r-fdb-infiniummethylation-hg19") |
| 660 | (version "2.2.0") |
| 661 | (source (origin |
| 662 | (method url-fetch) |
| 663 | ;; We cannot use bioconductor-uri here because this tarball is |
| 664 | ;; located under "data/annotation/" instead of "bioc/". |
| 665 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 666 | "release/data/annotation/src/contrib/" |
| 667 | "FDb.InfiniumMethylation.hg19_" |
| 668 | version ".tar.gz")) |
| 669 | (sha256 |
| 670 | (base32 |
| 671 | "0gq90fvph6kgrpjb89nvzq6hl1k24swn19rgjh5g98l86mja6nk0")))) |
| 672 | (properties |
| 673 | `((upstream-name . "FDb.InfiniumMethylation.hg19"))) |
| 674 | (build-system r-build-system) |
| 675 | (propagated-inputs |
| 676 | `(("r-biostrings" ,r-biostrings) |
| 677 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 678 | ("r-annotationdbi" ,r-annotationdbi) |
| 679 | ("r-org-hs-eg-db" ,r-org-hs-eg-db) |
| 680 | ("r-txdb-hsapiens-ucsc-hg19-knowngene" ,r-txdb-hsapiens-ucsc-hg19-knowngene))) |
| 681 | (home-page "https://bioconductor.org/packages/FDb.InfiniumMethylation.hg19/") |
| 682 | (synopsis "Compiled HumanMethylation27 and HumanMethylation450 annotations") |
| 683 | (description |
| 684 | "This is an annotation package for Illumina Infinium DNA methylation |
| 685 | probes. It contains the compiled HumanMethylation27 and HumanMethylation450 |
| 686 | annotations.") |
| 687 | (license license:artistic2.0))) |
| 688 | |
| 689 | (define-public r-illuminahumanmethylationepicmanifest |
| 690 | (package |
| 691 | (name "r-illuminahumanmethylationepicmanifest") |
| 692 | (version "0.3.0") |
| 693 | (source (origin |
| 694 | (method url-fetch) |
| 695 | ;; We cannot use bioconductor-uri here because this tarball is |
| 696 | ;; located under "data/annotation/" instead of "bioc/". |
| 697 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 698 | "release/data/annotation/src/contrib/" |
| 699 | "IlluminaHumanMethylationEPICmanifest_" |
| 700 | version ".tar.gz")) |
| 701 | (sha256 |
| 702 | (base32 |
| 703 | "0alhjda5g186z8b1nsmnpfswrlj7prdz8mkwx60wkkl6hkcnk6p3")))) |
| 704 | (properties |
| 705 | `((upstream-name . "IlluminaHumanMethylationEPICmanifest"))) |
| 706 | (build-system r-build-system) |
| 707 | (propagated-inputs |
| 708 | `(("r-minfi" ,r-minfi))) |
| 709 | (home-page "https://bioconductor.org/packages/IlluminaHumanMethylationEPICmanifest/") |
| 710 | (synopsis "Manifest for Illumina's EPIC methylation arrays") |
| 711 | (description |
| 712 | "This is a manifest package for Illumina's EPIC methylation arrays.") |
| 713 | (license license:artistic2.0))) |
| 714 | |
| 715 | (define-public r-do-db |
| 716 | (package |
| 717 | (name "r-do-db") |
| 718 | (version "2.9") |
| 719 | (source (origin |
| 720 | (method url-fetch) |
| 721 | ;; We cannot use bioconductor-uri here because this tarball is |
| 722 | ;; located under "data/annotation/" instead of "bioc/". |
| 723 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 724 | "release/data/annotation/src/contrib/" |
| 725 | "DO.db_" version ".tar.gz")) |
| 726 | (sha256 |
| 727 | (base32 |
| 728 | "10bqqa124l61ivzy4mdd3z3ar9a6537qbxw23pc4y9w8a6dwnavn")))) |
| 729 | (properties |
| 730 | `((upstream-name . "DO.db"))) |
| 731 | (build-system r-build-system) |
| 732 | (propagated-inputs |
| 733 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 734 | (home-page "https://www.bioconductor.org/packages/DO.db/") |
| 735 | (synopsis "Annotation maps describing the entire Disease Ontology") |
| 736 | (description |
| 737 | "This package provides a set of annotation maps describing the entire |
| 738 | Disease Ontology.") |
| 739 | (license license:artistic2.0))) |
| 740 | |
| 741 | \f |
| 742 | ;;; Experiment data |
| 743 | |
| 744 | (define-public r-abadata |
| 745 | (package |
| 746 | (name "r-abadata") |
| 747 | (version "1.12.0") |
| 748 | (source (origin |
| 749 | (method url-fetch) |
| 750 | ;; We cannot use bioconductor-uri here because this tarball is |
| 751 | ;; located under "data/experiment/" instead of "bioc/". |
| 752 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 753 | "release/data/experiment/src/contrib/" |
| 754 | "ABAData_" version ".tar.gz")) |
| 755 | (sha256 |
| 756 | (base32 |
| 757 | "1bmj341xcymlrk02gss5vvrqc4ddas0rdw39lnpsj98hq6n11p5z")))) |
| 758 | (properties |
| 759 | `((upstream-name . "ABAData"))) |
| 760 | (build-system r-build-system) |
| 761 | (propagated-inputs |
| 762 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 763 | (home-page "https://www.bioconductor.org/packages/ABAData/") |
| 764 | (synopsis "Gene expression in human brain regions from Allen Brain Atlas") |
| 765 | (description |
| 766 | "This package provides the data for the gene expression enrichment |
| 767 | analysis conducted in the package ABAEnrichment. The package includes three |
| 768 | datasets which are derived from the Allen Brain Atlas: |
| 769 | |
| 770 | @enumerate |
| 771 | @item Gene expression data from Human Brain (adults) averaged across donors, |
| 772 | @item Gene expression data from the Developing Human Brain pooled into five |
| 773 | age categories and averaged across donors, and |
| 774 | @item a developmental effect score based on the Developing Human Brain |
| 775 | expression data. |
| 776 | @end enumerate |
| 777 | |
| 778 | All datasets are restricted to protein coding genes.") |
| 779 | (license license:gpl2+))) |
| 780 | |
| 781 | (define-public r-arrmdata |
| 782 | (package |
| 783 | (name "r-arrmdata") |
| 784 | (version "1.18.0") |
| 785 | (source (origin |
| 786 | (method url-fetch) |
| 787 | ;; We cannot use bioconductor-uri here because this tarball is |
| 788 | ;; located under "data/experiment/" instead of "bioc/". |
| 789 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 790 | "release/data/experiment/src/contrib/" |
| 791 | "ARRmData_" version ".tar.gz")) |
| 792 | (sha256 |
| 793 | (base32 |
| 794 | "0r1y3zn7ly4k3ngx55vfavn9s6aidbddlv2fbmj7hj3hvpslmyly")))) |
| 795 | (properties |
| 796 | `((upstream-name . "ARRmData"))) |
| 797 | (build-system r-build-system) |
| 798 | (home-page "https://www.bioconductor.org/packages/ARRmData/") |
| 799 | (synopsis "Example dataset for normalization of Illumina 450k methylation data") |
| 800 | (description |
| 801 | "This package provides raw beta values from 36 samples across 3 groups |
| 802 | from Illumina 450k methylation arrays.") |
| 803 | (license license:artistic2.0))) |
| 804 | |
| 805 | (define-public r-hsmmsinglecell |
| 806 | (package |
| 807 | (name "r-hsmmsinglecell") |
| 808 | (version "1.2.0") |
| 809 | (source (origin |
| 810 | (method url-fetch) |
| 811 | ;; We cannot use bioconductor-uri here because this tarball is |
| 812 | ;; located under "data/experiment/" instead of "bioc/". |
| 813 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 814 | "release/data/experiment/src/contrib/" |
| 815 | "HSMMSingleCell_" version ".tar.gz")) |
| 816 | (sha256 |
| 817 | (base32 |
| 818 | "1vxnr8gr6md85g39csy7g2sqqajiqgyvznys2qa9yixd2b01yph9")))) |
| 819 | (properties |
| 820 | `((upstream-name . "HSMMSingleCell"))) |
| 821 | (build-system r-build-system) |
| 822 | (home-page "https://www.bioconductor.org/packages/HSMMSingleCell/") |
| 823 | (synopsis "Single-cell RNA-Seq for differentiating human skeletal muscle myoblasts (HSMM)") |
| 824 | (description |
| 825 | "Skeletal myoblasts undergo a well-characterized sequence of |
| 826 | morphological and transcriptional changes during differentiation. In this |
| 827 | experiment, primary @dfn{human skeletal muscle myoblasts} (HSMM) were expanded |
| 828 | under high mitogen conditions (GM) and then differentiated by switching to |
| 829 | low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several |
| 830 | hundred cells taken over a time-course of serum-induced differentiation. |
| 831 | Between 49 and 77 cells were captured at each of four time points (0, 24, 48, |
| 832 | 72 hours) following serum switch using the Fluidigm C1 microfluidic system. |
| 833 | RNA from each cell was isolated and used to construct mRNA-Seq libraries, |
| 834 | which were then sequenced to a depth of ~4 million reads per library, |
| 835 | resulting in a complete gene expression profile for each cell.") |
| 836 | (license license:artistic2.0))) |
| 837 | |
| 838 | \f |
| 839 | ;;; Packages |
| 840 | |
| 841 | (define-public r-biocgenerics |
| 842 | (package |
| 843 | (name "r-biocgenerics") |
| 844 | (version "0.30.0") |
| 845 | (source (origin |
| 846 | (method url-fetch) |
| 847 | (uri (bioconductor-uri "BiocGenerics" version)) |
| 848 | (sha256 |
| 849 | (base32 |
| 850 | "1n87686bg5nmpqdpzwv1h551dkbxp9wk6wbmzpkgm71qxnk2yv9f")))) |
| 851 | (properties |
| 852 | `((upstream-name . "BiocGenerics"))) |
| 853 | (build-system r-build-system) |
| 854 | (home-page "https://bioconductor.org/packages/BiocGenerics") |
| 855 | (synopsis "S4 generic functions for Bioconductor") |
| 856 | (description |
| 857 | "This package provides S4 generic functions needed by many Bioconductor |
| 858 | packages.") |
| 859 | (license license:artistic2.0))) |
| 860 | |
| 861 | (define-public r-annotate |
| 862 | (package |
| 863 | (name "r-annotate") |
| 864 | (version "1.62.0") |
| 865 | (source |
| 866 | (origin |
| 867 | (method url-fetch) |
| 868 | (uri (bioconductor-uri "annotate" version)) |
| 869 | (sha256 |
| 870 | (base32 |
| 871 | "0hww0h4b7bv37mnjviazy247mnzj72z5linwm1gvljrgqv3bagcs")))) |
| 872 | (build-system r-build-system) |
| 873 | (propagated-inputs |
| 874 | `(("r-annotationdbi" ,r-annotationdbi) |
| 875 | ("r-biobase" ,r-biobase) |
| 876 | ("r-biocgenerics" ,r-biocgenerics) |
| 877 | ("r-dbi" ,r-dbi) |
| 878 | ("r-rcurl" ,r-rcurl) |
| 879 | ("r-xml" ,r-xml) |
| 880 | ("r-xtable" ,r-xtable))) |
| 881 | (home-page |
| 882 | "https://bioconductor.org/packages/annotate") |
| 883 | (synopsis "Annotation for microarrays") |
| 884 | (description "This package provides R environments for the annotation of |
| 885 | microarrays.") |
| 886 | (license license:artistic2.0))) |
| 887 | |
| 888 | (define-public r-hpar |
| 889 | (package |
| 890 | (name "r-hpar") |
| 891 | (version "1.26.0") |
| 892 | (source |
| 893 | (origin |
| 894 | (method url-fetch) |
| 895 | (uri (bioconductor-uri "hpar" version)) |
| 896 | (sha256 |
| 897 | (base32 |
| 898 | "1mnld60nrn6qpb24sz2sy8vlw3wkhfc3z726gi67l8b5mdmkxgg5")))) |
| 899 | (build-system r-build-system) |
| 900 | (home-page "https://bioconductor.org/packages/hpar/") |
| 901 | (synopsis "Human Protein Atlas in R") |
| 902 | (description "This package provides a simple interface to and data from |
| 903 | the Human Protein Atlas project.") |
| 904 | (license license:artistic2.0))) |
| 905 | |
| 906 | (define-public r-regioner |
| 907 | (package |
| 908 | (name "r-regioner") |
| 909 | (version "1.16.0") |
| 910 | (source |
| 911 | (origin |
| 912 | (method url-fetch) |
| 913 | (uri (bioconductor-uri "regioneR" version)) |
| 914 | (sha256 |
| 915 | (base32 |
| 916 | "014h2q346ynfdbpavh4p69cyv4j65hk934liq5892zznjzl73z7p")))) |
| 917 | (properties `((upstream-name . "regioneR"))) |
| 918 | (build-system r-build-system) |
| 919 | (propagated-inputs |
| 920 | `(("r-biostrings" ,r-biostrings) |
| 921 | ("r-bsgenome" ,r-bsgenome) |
| 922 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 923 | ("r-genomicranges" ,r-genomicranges) |
| 924 | ("r-iranges" ,r-iranges) |
| 925 | ("r-memoise" ,r-memoise) |
| 926 | ("r-rtracklayer" ,r-rtracklayer) |
| 927 | ("r-s4vectors" ,r-s4vectors))) |
| 928 | (home-page "https://bioconductor.org/packages/regioneR/") |
| 929 | (synopsis "Association analysis of genomic regions") |
| 930 | (description "This package offers a statistical framework based on |
| 931 | customizable permutation tests to assess the association between genomic |
| 932 | region sets and other genomic features.") |
| 933 | (license license:artistic2.0))) |
| 934 | |
| 935 | (define-public r-geneplotter |
| 936 | (package |
| 937 | (name "r-geneplotter") |
| 938 | (version "1.62.0") |
| 939 | (source |
| 940 | (origin |
| 941 | (method url-fetch) |
| 942 | (uri (bioconductor-uri "geneplotter" version)) |
| 943 | (sha256 |
| 944 | (base32 |
| 945 | "0jlqs20mqr0wgmjgzkzaynp3cy1z3xjzpz7055c1qi42fhimmimb")))) |
| 946 | (build-system r-build-system) |
| 947 | (propagated-inputs |
| 948 | `(("r-annotate" ,r-annotate) |
| 949 | ("r-annotationdbi" ,r-annotationdbi) |
| 950 | ("r-biobase" ,r-biobase) |
| 951 | ("r-biocgenerics" ,r-biocgenerics) |
| 952 | ("r-lattice" ,r-lattice) |
| 953 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 954 | (home-page "https://bioconductor.org/packages/geneplotter") |
| 955 | (synopsis "Graphics functions for genomic data") |
| 956 | (description |
| 957 | "This package provides functions for plotting genomic data.") |
| 958 | (license license:artistic2.0))) |
| 959 | |
| 960 | (define-public r-qvalue |
| 961 | (package |
| 962 | (name "r-qvalue") |
| 963 | (version "2.16.0") |
| 964 | (source |
| 965 | (origin |
| 966 | (method url-fetch) |
| 967 | (uri (bioconductor-uri "qvalue" version)) |
| 968 | (sha256 |
| 969 | (base32 |
| 970 | "00mahhwb4n2s6nycwkdkjs2qgyyyi7hyrby3qr269krprr6q3lh5")))) |
| 971 | (build-system r-build-system) |
| 972 | (propagated-inputs |
| 973 | `(("r-ggplot2" ,r-ggplot2) |
| 974 | ("r-reshape2" ,r-reshape2))) |
| 975 | (home-page "http://github.com/jdstorey/qvalue") |
| 976 | (synopsis "Q-value estimation for false discovery rate control") |
| 977 | (description |
| 978 | "This package takes a list of p-values resulting from the simultaneous |
| 979 | testing of many hypotheses and estimates their q-values and local @dfn{false |
| 980 | discovery rate} (FDR) values. The q-value of a test measures the proportion |
| 981 | of false positives incurred when that particular test is called significant. |
| 982 | The local FDR measures the posterior probability the null hypothesis is true |
| 983 | given the test's p-value. Various plots are automatically generated, allowing |
| 984 | one to make sensible significance cut-offs. The software can be applied to |
| 985 | problems in genomics, brain imaging, astrophysics, and data mining.") |
| 986 | ;; Any version of the LGPL. |
| 987 | (license license:lgpl3+))) |
| 988 | |
| 989 | (define-public r-diffbind |
| 990 | (package |
| 991 | (name "r-diffbind") |
| 992 | (version "2.12.0") |
| 993 | (source |
| 994 | (origin |
| 995 | (method url-fetch) |
| 996 | (uri (bioconductor-uri "DiffBind" version)) |
| 997 | (sha256 |
| 998 | (base32 |
| 999 | "1ialb1j2xa21a8dzss76qky83rg8y6jwdwi0mhy8b088zvxavich")))) |
| 1000 | (properties `((upstream-name . "DiffBind"))) |
| 1001 | (build-system r-build-system) |
| 1002 | (inputs |
| 1003 | `(("zlib" ,zlib))) |
| 1004 | (propagated-inputs |
| 1005 | `(("r-amap" ,r-amap) |
| 1006 | ("r-biocparallel" ,r-biocparallel) |
| 1007 | ("r-deseq2" ,r-deseq2) |
| 1008 | ("r-dplyr" ,r-dplyr) |
| 1009 | ("r-edger" ,r-edger) |
| 1010 | ("r-genomicalignments" ,r-genomicalignments) |
| 1011 | ("r-genomicranges" ,r-genomicranges) |
| 1012 | ("r-ggplot2" ,r-ggplot2) |
| 1013 | ("r-ggrepel" ,r-ggrepel) |
| 1014 | ("r-gplots" ,r-gplots) |
| 1015 | ("r-iranges" ,r-iranges) |
| 1016 | ("r-lattice" ,r-lattice) |
| 1017 | ("r-limma" ,r-limma) |
| 1018 | ("r-locfit" ,r-locfit) |
| 1019 | ("r-rcolorbrewer" , r-rcolorbrewer) |
| 1020 | ("r-rcpp" ,r-rcpp) |
| 1021 | ("r-rhtslib" ,r-rhtslib) |
| 1022 | ("r-rsamtools" ,r-rsamtools) |
| 1023 | ("r-s4vectors" ,r-s4vectors) |
| 1024 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 1025 | ("r-systempiper" ,r-systempiper))) |
| 1026 | (home-page "http://bioconductor.org/packages/DiffBind") |
| 1027 | (synopsis "Differential binding analysis of ChIP-Seq peak data") |
| 1028 | (description |
| 1029 | "This package computes differentially bound sites from multiple |
| 1030 | ChIP-seq experiments using affinity (quantitative) data. Also enables |
| 1031 | occupancy (overlap) analysis and plotting functions.") |
| 1032 | (license license:artistic2.0))) |
| 1033 | |
| 1034 | (define-public r-ripseeker |
| 1035 | (package |
| 1036 | (name "r-ripseeker") |
| 1037 | (version "1.24.0") |
| 1038 | (source |
| 1039 | (origin |
| 1040 | (method url-fetch) |
| 1041 | (uri (bioconductor-uri "RIPSeeker" version)) |
| 1042 | (sha256 |
| 1043 | (base32 |
| 1044 | "0rfff4wal51iji0m74mgnrlcq6i41nq5b79mv5brv7mab3g0cv43")))) |
| 1045 | (properties `((upstream-name . "RIPSeeker"))) |
| 1046 | (build-system r-build-system) |
| 1047 | (propagated-inputs |
| 1048 | `(("r-s4vectors" ,r-s4vectors) |
| 1049 | ("r-iranges" ,r-iranges) |
| 1050 | ("r-genomicranges" ,r-genomicranges) |
| 1051 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 1052 | ("r-rsamtools" ,r-rsamtools) |
| 1053 | ("r-genomicalignments" ,r-genomicalignments) |
| 1054 | ("r-rtracklayer" ,r-rtracklayer))) |
| 1055 | (home-page "http://bioconductor.org/packages/RIPSeeker") |
| 1056 | (synopsis |
| 1057 | "Identifying protein-associated transcripts from RIP-seq experiments") |
| 1058 | (description |
| 1059 | "This package infers and discriminates RIP peaks from RIP-seq alignments |
| 1060 | using two-state HMM with negative binomial emission probability. While |
| 1061 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides |
| 1062 | a suite of bioinformatics tools integrated within this self-contained software |
| 1063 | package comprehensively addressing issues ranging from post-alignments |
| 1064 | processing to visualization and annotation.") |
| 1065 | (license license:gpl2))) |
| 1066 | |
| 1067 | (define-public r-multtest |
| 1068 | (package |
| 1069 | (name "r-multtest") |
| 1070 | (version "2.40.0") |
| 1071 | (source |
| 1072 | (origin |
| 1073 | (method url-fetch) |
| 1074 | (uri (bioconductor-uri "multtest" version)) |
| 1075 | (sha256 |
| 1076 | (base32 |
| 1077 | "0vy9wk1111qm69xy4r4n01b9rw60dsrcj2169jd45yiq63cdq7bv")))) |
| 1078 | (build-system r-build-system) |
| 1079 | (propagated-inputs |
| 1080 | `(("r-survival" ,r-survival) |
| 1081 | ("r-biocgenerics" ,r-biocgenerics) |
| 1082 | ("r-biobase" ,r-biobase) |
| 1083 | ("r-mass" ,r-mass))) |
| 1084 | (home-page "http://bioconductor.org/packages/multtest") |
| 1085 | (synopsis "Resampling-based multiple hypothesis testing") |
| 1086 | (description |
| 1087 | "This package can do non-parametric bootstrap and permutation |
| 1088 | resampling-based multiple testing procedures (including empirical Bayes |
| 1089 | methods) for controlling the family-wise error rate (FWER), generalized |
| 1090 | family-wise error rate (gFWER), tail probability of the proportion of |
| 1091 | false positives (TPPFP), and false discovery rate (FDR). Several choices |
| 1092 | of bootstrap-based null distribution are implemented (centered, centered |
| 1093 | and scaled, quantile-transformed). Single-step and step-wise methods are |
| 1094 | available. Tests based on a variety of T- and F-statistics (including |
| 1095 | T-statistics based on regression parameters from linear and survival models |
| 1096 | as well as those based on correlation parameters) are included. When probing |
| 1097 | hypotheses with T-statistics, users may also select a potentially faster null |
| 1098 | distribution which is multivariate normal with mean zero and variance |
| 1099 | covariance matrix derived from the vector influence function. Results are |
| 1100 | reported in terms of adjusted P-values, confidence regions and test statistic |
| 1101 | cutoffs. The procedures are directly applicable to identifying differentially |
| 1102 | expressed genes in DNA microarray experiments.") |
| 1103 | (license license:lgpl3))) |
| 1104 | |
| 1105 | (define-public r-graph |
| 1106 | (package |
| 1107 | (name "r-graph") |
| 1108 | (version "1.62.0") |
| 1109 | (source (origin |
| 1110 | (method url-fetch) |
| 1111 | (uri (bioconductor-uri "graph" version)) |
| 1112 | (sha256 |
| 1113 | (base32 |
| 1114 | "0rs81a8kp7nfzsfy2d11mlrjf4z156075p52wvz9nvi3vc6l348w")))) |
| 1115 | (build-system r-build-system) |
| 1116 | (propagated-inputs |
| 1117 | `(("r-biocgenerics" ,r-biocgenerics))) |
| 1118 | (home-page "https://bioconductor.org/packages/graph") |
| 1119 | (synopsis "Handle graph data structures in R") |
| 1120 | (description |
| 1121 | "This package implements some simple graph handling capabilities for R.") |
| 1122 | (license license:artistic2.0))) |
| 1123 | |
| 1124 | (define-public r-codedepends |
| 1125 | (package |
| 1126 | (name "r-codedepends") |
| 1127 | (version "0.6.5") |
| 1128 | (source |
| 1129 | (origin |
| 1130 | (method url-fetch) |
| 1131 | (uri (cran-uri "CodeDepends" version)) |
| 1132 | (sha256 |
| 1133 | (base32 |
| 1134 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) |
| 1135 | (properties `((upstream-name . "CodeDepends"))) |
| 1136 | (build-system r-build-system) |
| 1137 | (propagated-inputs |
| 1138 | `(("r-codetools" ,r-codetools) |
| 1139 | ("r-graph" ,r-graph) |
| 1140 | ("r-xml" ,r-xml))) |
| 1141 | (home-page "http://cran.r-project.org/web/packages/CodeDepends") |
| 1142 | (synopsis "Analysis of R code for reproducible research and code comprehension") |
| 1143 | (description |
| 1144 | "This package provides tools for analyzing R expressions or blocks of |
| 1145 | code and determining the dependencies between them. It focuses on R scripts, |
| 1146 | but can be used on the bodies of functions. There are many facilities |
| 1147 | including the ability to summarize or get a high-level view of code, |
| 1148 | determining dependencies between variables, code improvement suggestions.") |
| 1149 | ;; Any version of the GPL |
| 1150 | (license (list license:gpl2+ license:gpl3+)))) |
| 1151 | |
| 1152 | (define-public r-chippeakanno |
| 1153 | (package |
| 1154 | (name "r-chippeakanno") |
| 1155 | (version "3.16.1") |
| 1156 | (source |
| 1157 | (origin |
| 1158 | (method url-fetch) |
| 1159 | (uri (bioconductor-uri "ChIPpeakAnno" version)) |
| 1160 | (sha256 |
| 1161 | (base32 |
| 1162 | "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3")))) |
| 1163 | (properties `((upstream-name . "ChIPpeakAnno"))) |
| 1164 | (build-system r-build-system) |
| 1165 | (propagated-inputs |
| 1166 | `(("r-biocgenerics" ,r-biocgenerics) |
| 1167 | ("r-biocmanager" ,r-biocmanager) |
| 1168 | ("r-biostrings" ,r-biostrings) |
| 1169 | ("r-delayedarray" ,r-delayedarray) |
| 1170 | ("r-go-db" ,r-go-db) |
| 1171 | ("r-biomart" ,r-biomart) |
| 1172 | ("r-bsgenome" ,r-bsgenome) |
| 1173 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 1174 | ("r-genomicranges" ,r-genomicranges) |
| 1175 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1176 | ("r-iranges" ,r-iranges) |
| 1177 | ("r-matrixstats" ,r-matrixstats) |
| 1178 | ("r-annotationdbi" ,r-annotationdbi) |
| 1179 | ("r-limma" ,r-limma) |
| 1180 | ("r-multtest" ,r-multtest) |
| 1181 | ("r-rbgl" ,r-rbgl) |
| 1182 | ("r-graph" ,r-graph) |
| 1183 | ("r-regioner" ,r-regioner) |
| 1184 | ("r-dbi" ,r-dbi) |
| 1185 | ("r-ensembldb" ,r-ensembldb) |
| 1186 | ("r-biobase" ,r-biobase) |
| 1187 | ("r-s4vectors" ,r-s4vectors) |
| 1188 | ("r-seqinr" ,r-seqinr) |
| 1189 | ("r-idr" ,r-idr) |
| 1190 | ("r-genomicalignments" ,r-genomicalignments) |
| 1191 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 1192 | ("r-rsamtools" ,r-rsamtools) |
| 1193 | ("r-venndiagram" ,r-venndiagram))) |
| 1194 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") |
| 1195 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") |
| 1196 | (description |
| 1197 | "The package includes functions to retrieve the sequences around the peak, |
| 1198 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or |
| 1199 | custom features such as most conserved elements and other transcription factor |
| 1200 | binding sites supplied by users. Starting 2.0.5, new functions have been added |
| 1201 | for finding the peaks with bi-directional promoters with summary statistics |
| 1202 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks |
| 1203 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or |
| 1204 | enrichedGO (addGeneIDs).") |
| 1205 | (license license:gpl2+))) |
| 1206 | |
| 1207 | (define-public r-marray |
| 1208 | (package |
| 1209 | (name "r-marray") |
| 1210 | (version "1.62.0") |
| 1211 | (source (origin |
| 1212 | (method url-fetch) |
| 1213 | (uri (bioconductor-uri "marray" version)) |
| 1214 | (sha256 |
| 1215 | (base32 "000745d7gxka8cx4jwxf0p128jk90dw6wi3y8dkrkyz2arkl29yz")))) |
| 1216 | (build-system r-build-system) |
| 1217 | (propagated-inputs |
| 1218 | `(("r-limma" ,r-limma))) |
| 1219 | (home-page "http://bioconductor.org/packages/marray") |
| 1220 | (synopsis "Exploratory analysis for two-color spotted microarray data") |
| 1221 | (description "This package contains class definitions for two-color spotted |
| 1222 | microarray data. It also includes fuctions for data input, diagnostic plots, |
| 1223 | normalization and quality checking.") |
| 1224 | (license license:lgpl2.0+))) |
| 1225 | |
| 1226 | (define-public r-cghbase |
| 1227 | (package |
| 1228 | (name "r-cghbase") |
| 1229 | (version "1.44.0") |
| 1230 | (source (origin |
| 1231 | (method url-fetch) |
| 1232 | (uri (bioconductor-uri "CGHbase" version)) |
| 1233 | (sha256 |
| 1234 | (base32 "0z9lvn5dxym6kc8ak5fsqkipv2p4z49va3cyz1ch8rw477k2iwvm")))) |
| 1235 | (properties `((upstream-name . "CGHbase"))) |
| 1236 | (build-system r-build-system) |
| 1237 | (propagated-inputs |
| 1238 | `(("r-biobase" ,r-biobase) |
| 1239 | ("r-marray" ,r-marray))) |
| 1240 | (home-page "http://bioconductor.org/packages/CGHbase") |
| 1241 | (synopsis "Base functions and classes for arrayCGH data analysis") |
| 1242 | (description "This package contains functions and classes that are needed by |
| 1243 | the @code{arrayCGH} packages.") |
| 1244 | (license license:gpl2+))) |
| 1245 | |
| 1246 | (define-public r-cghcall |
| 1247 | (package |
| 1248 | (name "r-cghcall") |
| 1249 | (version "2.46.0") |
| 1250 | (source (origin |
| 1251 | (method url-fetch) |
| 1252 | (uri (bioconductor-uri "CGHcall" version)) |
| 1253 | (sha256 |
| 1254 | (base32 "13vzk4myizs94hyak4iyxdrqyxyq1g85hwsmd13892g8pww6ga93")))) |
| 1255 | (properties `((upstream-name . "CGHcall"))) |
| 1256 | (build-system r-build-system) |
| 1257 | (propagated-inputs |
| 1258 | `(("r-biobase" ,r-biobase) |
| 1259 | ("r-cghbase" ,r-cghbase) |
| 1260 | ("r-impute" ,r-impute) |
| 1261 | ("r-dnacopy" ,r-dnacopy) |
| 1262 | ("r-snowfall" ,r-snowfall))) |
| 1263 | (home-page "http://bioconductor.org/packages/CGHcall") |
| 1264 | (synopsis "Base functions and classes for arrayCGH data analysis") |
| 1265 | (description "This package contains functions and classes that are needed by |
| 1266 | @code{arrayCGH} packages.") |
| 1267 | (license license:gpl2+))) |
| 1268 | |
| 1269 | (define-public r-qdnaseq |
| 1270 | (package |
| 1271 | (name "r-qdnaseq") |
| 1272 | (version "1.20.0") |
| 1273 | (source (origin |
| 1274 | (method url-fetch) |
| 1275 | (uri (bioconductor-uri "QDNAseq" version)) |
| 1276 | (sha256 |
| 1277 | (base32 "02afy5bpj35981q1qm59jx399hksk6a9v1jfwy7x888rn86gfcfz")))) |
| 1278 | (properties `((upstream-name . "QDNAseq"))) |
| 1279 | (build-system r-build-system) |
| 1280 | (propagated-inputs |
| 1281 | `(("r-biobase" ,r-biobase) |
| 1282 | ("r-biocparallel" ,r-biocparallel) |
| 1283 | ("r-cghbase" ,r-cghbase) |
| 1284 | ("r-cghcall" ,r-cghcall) |
| 1285 | ("r-dnacopy" ,r-dnacopy) |
| 1286 | ("r-genomicranges" ,r-genomicranges) |
| 1287 | ("r-iranges" ,r-iranges) |
| 1288 | ("r-matrixstats" ,r-matrixstats) |
| 1289 | ("r-r-utils" ,r-r-utils) |
| 1290 | ("r-rsamtools" ,r-rsamtools))) |
| 1291 | (home-page "http://bioconductor.org/packages/QDNAseq") |
| 1292 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") |
| 1293 | (description "The genome is divided into non-overlapping fixed-sized bins, |
| 1294 | number of sequence reads in each counted, adjusted with a simultaneous |
| 1295 | two-dimensional loess correction for sequence mappability and GC content, and |
| 1296 | filtered to remove spurious regions in the genome. Downstream steps of |
| 1297 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, |
| 1298 | respectively.") |
| 1299 | (license license:gpl2+))) |
| 1300 | |
| 1301 | (define-public r-bayseq |
| 1302 | (package |
| 1303 | (name "r-bayseq") |
| 1304 | (version "2.18.0") |
| 1305 | (source |
| 1306 | (origin |
| 1307 | (method url-fetch) |
| 1308 | (uri (bioconductor-uri "baySeq" version)) |
| 1309 | (sha256 |
| 1310 | (base32 |
| 1311 | "13lm7n5zqw8yg5sqb92h6ppcnr0l32qdgmv7i16pn32fb6z41p0w")))) |
| 1312 | (properties `((upstream-name . "baySeq"))) |
| 1313 | (build-system r-build-system) |
| 1314 | (propagated-inputs |
| 1315 | `(("r-abind" ,r-abind) |
| 1316 | ("r-edger" ,r-edger) |
| 1317 | ("r-genomicranges" ,r-genomicranges))) |
| 1318 | (home-page "https://bioconductor.org/packages/baySeq/") |
| 1319 | (synopsis "Bayesian analysis of differential expression patterns in count data") |
| 1320 | (description |
| 1321 | "This package identifies differential expression in high-throughput count |
| 1322 | data, such as that derived from next-generation sequencing machines, |
| 1323 | calculating estimated posterior likelihoods of differential expression (or |
| 1324 | more complex hypotheses) via empirical Bayesian methods.") |
| 1325 | (license license:gpl3))) |
| 1326 | |
| 1327 | (define-public r-chipcomp |
| 1328 | (package |
| 1329 | (name "r-chipcomp") |
| 1330 | (version "1.14.0") |
| 1331 | (source |
| 1332 | (origin |
| 1333 | (method url-fetch) |
| 1334 | (uri (bioconductor-uri "ChIPComp" version)) |
| 1335 | (sha256 |
| 1336 | (base32 |
| 1337 | "0ragyl9dhg0ymgkh4z9d1cbwhbpcwh6x4985laaw6wmq2sjm732y")))) |
| 1338 | (properties `((upstream-name . "ChIPComp"))) |
| 1339 | (build-system r-build-system) |
| 1340 | (propagated-inputs |
| 1341 | `(("r-biocgenerics" ,r-biocgenerics) |
| 1342 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 1343 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) |
| 1344 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1345 | ("r-genomicranges" ,r-genomicranges) |
| 1346 | ("r-iranges" ,r-iranges) |
| 1347 | ("r-limma" ,r-limma) |
| 1348 | ("r-rsamtools" ,r-rsamtools) |
| 1349 | ("r-rtracklayer" ,r-rtracklayer) |
| 1350 | ("r-s4vectors" ,r-s4vectors))) |
| 1351 | (home-page "https://bioconductor.org/packages/ChIPComp") |
| 1352 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") |
| 1353 | (description |
| 1354 | "ChIPComp implements a statistical method for quantitative comparison of |
| 1355 | multiple ChIP-seq datasets. It detects differentially bound sharp binding |
| 1356 | sites across multiple conditions considering matching control in ChIP-seq |
| 1357 | datasets.") |
| 1358 | ;; Any version of the GPL. |
| 1359 | (license license:gpl3+))) |
| 1360 | |
| 1361 | (define-public r-riboprofiling |
| 1362 | (package |
| 1363 | (name "r-riboprofiling") |
| 1364 | (version "1.14.0") |
| 1365 | (source |
| 1366 | (origin |
| 1367 | (method url-fetch) |
| 1368 | (uri (bioconductor-uri "RiboProfiling" version)) |
| 1369 | (sha256 |
| 1370 | (base32 |
| 1371 | "1si8zkznm0slvghk786qsp0wd6sns6hggrnz88ww9fcfvsqvzsy9")))) |
| 1372 | (properties `((upstream-name . "RiboProfiling"))) |
| 1373 | (build-system r-build-system) |
| 1374 | (propagated-inputs |
| 1375 | `(("r-biocgenerics" ,r-biocgenerics) |
| 1376 | ("r-biostrings" ,r-biostrings) |
| 1377 | ("r-data-table" ,r-data-table) |
| 1378 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1379 | ("r-genomicalignments" ,r-genomicalignments) |
| 1380 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 1381 | ("r-genomicranges" ,r-genomicranges) |
| 1382 | ("r-ggbio" ,r-ggbio) |
| 1383 | ("r-ggplot2" ,r-ggplot2) |
| 1384 | ("r-iranges" ,r-iranges) |
| 1385 | ("r-plyr" ,r-plyr) |
| 1386 | ("r-reshape2" ,r-reshape2) |
| 1387 | ("r-rsamtools" ,r-rsamtools) |
| 1388 | ("r-rtracklayer" ,r-rtracklayer) |
| 1389 | ("r-s4vectors" ,r-s4vectors) |
| 1390 | ("r-sqldf" ,r-sqldf))) |
| 1391 | (home-page "https://bioconductor.org/packages/RiboProfiling/") |
| 1392 | (synopsis "Ribosome profiling data analysis") |
| 1393 | (description "Starting with a BAM file, this package provides the |
| 1394 | necessary functions for quality assessment, read start position recalibration, |
| 1395 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting |
| 1396 | of count data: pairs, log fold-change, codon frequency and coverage |
| 1397 | assessment, principal component analysis on codon coverage.") |
| 1398 | (license license:gpl3))) |
| 1399 | |
| 1400 | (define-public r-riboseqr |
| 1401 | (package |
| 1402 | (name "r-riboseqr") |
| 1403 | (version "1.18.0") |
| 1404 | (source |
| 1405 | (origin |
| 1406 | (method url-fetch) |
| 1407 | (uri (bioconductor-uri "riboSeqR" version)) |
| 1408 | (sha256 |
| 1409 | (base32 |
| 1410 | "1d1v098w7fmnsmxfg3l7yndyyr7ajig00axiwg413lyg255is1ga")))) |
| 1411 | (properties `((upstream-name . "riboSeqR"))) |
| 1412 | (build-system r-build-system) |
| 1413 | (propagated-inputs |
| 1414 | `(("r-abind" ,r-abind) |
| 1415 | ("r-bayseq" ,r-bayseq) |
| 1416 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1417 | ("r-genomicranges" ,r-genomicranges) |
| 1418 | ("r-iranges" ,r-iranges) |
| 1419 | ("r-rsamtools" ,r-rsamtools) |
| 1420 | ("r-seqlogo" ,r-seqlogo))) |
| 1421 | (home-page "https://bioconductor.org/packages/riboSeqR/") |
| 1422 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") |
| 1423 | (description |
| 1424 | "This package provides plotting functions, frameshift detection and |
| 1425 | parsing of genetic sequencing data from ribosome profiling experiments.") |
| 1426 | (license license:gpl3))) |
| 1427 | |
| 1428 | (define-public r-interactionset |
| 1429 | (package |
| 1430 | (name "r-interactionset") |
| 1431 | (version "1.12.0") |
| 1432 | (source |
| 1433 | (origin |
| 1434 | (method url-fetch) |
| 1435 | (uri (bioconductor-uri "InteractionSet" version)) |
| 1436 | (sha256 |
| 1437 | (base32 |
| 1438 | "0djgfpp34l6w8mk5b8s4wh0l12s4nn0f9ifvc3dq4970f6hb55z6")))) |
| 1439 | (properties |
| 1440 | `((upstream-name . "InteractionSet"))) |
| 1441 | (build-system r-build-system) |
| 1442 | (propagated-inputs |
| 1443 | `(("r-biocgenerics" ,r-biocgenerics) |
| 1444 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1445 | ("r-genomicranges" ,r-genomicranges) |
| 1446 | ("r-iranges" ,r-iranges) |
| 1447 | ("r-matrix" ,r-matrix) |
| 1448 | ("r-rcpp" ,r-rcpp) |
| 1449 | ("r-s4vectors" ,r-s4vectors) |
| 1450 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 1451 | (home-page "https://bioconductor.org/packages/InteractionSet") |
| 1452 | (synopsis "Base classes for storing genomic interaction data") |
| 1453 | (description |
| 1454 | "This packages provides the @code{GInteractions}, |
| 1455 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
| 1456 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET |
| 1457 | experiments.") |
| 1458 | (license license:gpl3))) |
| 1459 | |
| 1460 | (define-public r-genomicinteractions |
| 1461 | (package |
| 1462 | (name "r-genomicinteractions") |
| 1463 | (version "1.18.0") |
| 1464 | (source |
| 1465 | (origin |
| 1466 | (method url-fetch) |
| 1467 | (uri (bioconductor-uri "GenomicInteractions" version)) |
| 1468 | (sha256 |
| 1469 | (base32 |
| 1470 | "0ipvm3c1cqd46n60lsrqzf6fx4b3lwia57jyfx9wcqqg205qj73b")))) |
| 1471 | (properties |
| 1472 | `((upstream-name . "GenomicInteractions"))) |
| 1473 | (build-system r-build-system) |
| 1474 | (propagated-inputs |
| 1475 | `(("r-biobase" ,r-biobase) |
| 1476 | ("r-biocgenerics" ,r-biocgenerics) |
| 1477 | ("r-data-table" ,r-data-table) |
| 1478 | ("r-dplyr" ,r-dplyr) |
| 1479 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1480 | ("r-genomicranges" ,r-genomicranges) |
| 1481 | ("r-ggplot2" ,r-ggplot2) |
| 1482 | ("r-gridextra" ,r-gridextra) |
| 1483 | ("r-gviz" ,r-gviz) |
| 1484 | ("r-igraph" ,r-igraph) |
| 1485 | ("r-interactionset" ,r-interactionset) |
| 1486 | ("r-iranges" ,r-iranges) |
| 1487 | ("r-rsamtools" ,r-rsamtools) |
| 1488 | ("r-rtracklayer" ,r-rtracklayer) |
| 1489 | ("r-s4vectors" ,r-s4vectors) |
| 1490 | ("r-stringr" ,r-stringr))) |
| 1491 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") |
| 1492 | (synopsis "R package for handling genomic interaction data") |
| 1493 | (description |
| 1494 | "This R package provides tools for handling genomic interaction data, |
| 1495 | such as ChIA-PET/Hi-C, annotating genomic features with interaction |
| 1496 | information and producing various plots and statistics.") |
| 1497 | (license license:gpl3))) |
| 1498 | |
| 1499 | (define-public r-ctc |
| 1500 | (package |
| 1501 | (name "r-ctc") |
| 1502 | (version "1.58.0") |
| 1503 | (source |
| 1504 | (origin |
| 1505 | (method url-fetch) |
| 1506 | (uri (bioconductor-uri "ctc" version)) |
| 1507 | (sha256 |
| 1508 | (base32 |
| 1509 | "15n5b6i18x14km5rdqiydxcak5cr5dr3adwwwc5kcqf5gkwmi3am")))) |
| 1510 | (build-system r-build-system) |
| 1511 | (propagated-inputs `(("r-amap" ,r-amap))) |
| 1512 | (home-page "https://bioconductor.org/packages/ctc/") |
| 1513 | (synopsis "Cluster and tree conversion") |
| 1514 | (description |
| 1515 | "This package provides tools for exporting and importing classification |
| 1516 | trees and clusters to other programs.") |
| 1517 | (license license:gpl2))) |
| 1518 | |
| 1519 | (define-public r-goseq |
| 1520 | (package |
| 1521 | (name "r-goseq") |
| 1522 | (version "1.36.0") |
| 1523 | (source |
| 1524 | (origin |
| 1525 | (method url-fetch) |
| 1526 | (uri (bioconductor-uri "goseq" version)) |
| 1527 | (sha256 |
| 1528 | (base32 |
| 1529 | "0h8kd3d7yfdq8padfb0k92crwxi5h9gvgv4l3pa8k8wn4kczvciw")))) |
| 1530 | (build-system r-build-system) |
| 1531 | (propagated-inputs |
| 1532 | `(("r-annotationdbi" ,r-annotationdbi) |
| 1533 | ("r-biasedurn" ,r-biasedurn) |
| 1534 | ("r-biocgenerics" ,r-biocgenerics) |
| 1535 | ("r-genelendatabase" ,r-genelendatabase) |
| 1536 | ("r-go-db" ,r-go-db) |
| 1537 | ("r-mgcv" ,r-mgcv))) |
| 1538 | (home-page "https://bioconductor.org/packages/goseq/") |
| 1539 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") |
| 1540 | (description |
| 1541 | "This package provides tools to detect Gene Ontology and/or other user |
| 1542 | defined categories which are over/under represented in RNA-seq data.") |
| 1543 | (license license:lgpl2.0+))) |
| 1544 | |
| 1545 | (define-public r-glimma |
| 1546 | (package |
| 1547 | (name "r-glimma") |
| 1548 | (version "1.12.0") |
| 1549 | (source |
| 1550 | (origin |
| 1551 | (method url-fetch) |
| 1552 | (uri (bioconductor-uri "Glimma" version)) |
| 1553 | (sha256 |
| 1554 | (base32 |
| 1555 | "11qg5khqspxldfgg6p3xsxys472ab8wwi2snwc6bdxczv1f2p56x")))) |
| 1556 | (properties `((upstream-name . "Glimma"))) |
| 1557 | (build-system r-build-system) |
| 1558 | (propagated-inputs |
| 1559 | `(("r-edger" ,r-edger) |
| 1560 | ("r-jsonlite" ,r-jsonlite) |
| 1561 | ("r-s4vectors" ,r-s4vectors))) |
| 1562 | (home-page "https://github.com/Shians/Glimma") |
| 1563 | (synopsis "Interactive HTML graphics") |
| 1564 | (description |
| 1565 | "This package generates interactive visualisations for analysis of |
| 1566 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an |
| 1567 | HTML page. The interactions are built on top of the popular static |
| 1568 | representations of analysis results in order to provide additional |
| 1569 | information.") |
| 1570 | (license license:lgpl3))) |
| 1571 | |
| 1572 | (define-public r-rots |
| 1573 | (package |
| 1574 | (name "r-rots") |
| 1575 | (version "1.12.0") |
| 1576 | (source |
| 1577 | (origin |
| 1578 | (method url-fetch) |
| 1579 | (uri (bioconductor-uri "ROTS" version)) |
| 1580 | (sha256 |
| 1581 | (base32 |
| 1582 | "1j29pfyv2pn0wp544m5a568b3yd31kzavwwiwqylcjwvq5lfzy77")))) |
| 1583 | (properties `((upstream-name . "ROTS"))) |
| 1584 | (build-system r-build-system) |
| 1585 | (propagated-inputs |
| 1586 | `(("r-biobase" ,r-biobase) |
| 1587 | ("r-rcpp" ,r-rcpp))) |
| 1588 | (home-page "https://bioconductor.org/packages/ROTS/") |
| 1589 | (synopsis "Reproducibility-Optimized Test Statistic") |
| 1590 | (description |
| 1591 | "This package provides tools for calculating the |
| 1592 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing |
| 1593 | in omics data.") |
| 1594 | (license license:gpl2+))) |
| 1595 | |
| 1596 | (define-public r-plgem |
| 1597 | (package |
| 1598 | (name "r-plgem") |
| 1599 | (version "1.56.0") |
| 1600 | (source |
| 1601 | (origin |
| 1602 | (method url-fetch) |
| 1603 | (uri (bioconductor-uri "plgem" version)) |
| 1604 | (sha256 |
| 1605 | (base32 |
| 1606 | "0y6gp5rlkvlv435qps7zhih84g5wrdvg6myj74ywnpl5a773nfqp")))) |
| 1607 | (build-system r-build-system) |
| 1608 | (propagated-inputs |
| 1609 | `(("r-biobase" ,r-biobase) |
| 1610 | ("r-mass" ,r-mass))) |
| 1611 | (home-page "http://www.genopolis.it") |
| 1612 | (synopsis "Detect differential expression in microarray and proteomics datasets") |
| 1613 | (description |
| 1614 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully |
| 1615 | model the variance-versus-mean dependence that exists in a variety of |
| 1616 | genome-wide datasets, including microarray and proteomics data. The use of |
| 1617 | PLGEM has been shown to improve the detection of differentially expressed |
| 1618 | genes or proteins in these datasets.") |
| 1619 | (license license:gpl2))) |
| 1620 | |
| 1621 | (define-public r-inspect |
| 1622 | (package |
| 1623 | (name "r-inspect") |
| 1624 | (version "1.14.0") |
| 1625 | (source |
| 1626 | (origin |
| 1627 | (method url-fetch) |
| 1628 | (uri (bioconductor-uri "INSPEcT" version)) |
| 1629 | (sha256 |
| 1630 | (base32 |
| 1631 | "1a7smljndiyahgpj6vl079pvi3n0rfk1vkdkp799y4nm2wnhn93r")))) |
| 1632 | (properties `((upstream-name . "INSPEcT"))) |
| 1633 | (build-system r-build-system) |
| 1634 | (propagated-inputs |
| 1635 | `(("r-biobase" ,r-biobase) |
| 1636 | ("r-biocgenerics" ,r-biocgenerics) |
| 1637 | ("r-biocparallel" ,r-biocparallel) |
| 1638 | ("r-deseq2" ,r-deseq2) |
| 1639 | ("r-desolve" ,r-desolve) |
| 1640 | ("r-genomicalignments" ,r-genomicalignments) |
| 1641 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 1642 | ("r-genomicranges" ,r-genomicranges) |
| 1643 | ("r-iranges" ,r-iranges) |
| 1644 | ("r-plgem" ,r-plgem) |
| 1645 | ("r-preprocesscore" ,r-preprocesscore) |
| 1646 | ("r-proc" ,r-proc) |
| 1647 | ("r-rootsolve" ,r-rootsolve) |
| 1648 | ("r-rsamtools" ,r-rsamtools) |
| 1649 | ("r-s4vectors" ,r-s4vectors) |
| 1650 | ("r-shiny" ,r-shiny) |
| 1651 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 1652 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" |
| 1653 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) |
| 1654 | (home-page "https://bioconductor.org/packages/INSPEcT") |
| 1655 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") |
| 1656 | (description |
| 1657 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in |
| 1658 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in |
| 1659 | order to evaluate synthesis, processing and degradation rates and assess via |
| 1660 | modeling the rates that determines changes in mature mRNA levels.") |
| 1661 | (license license:gpl2))) |
| 1662 | |
| 1663 | (define-public r-dnabarcodes |
| 1664 | (package |
| 1665 | (name "r-dnabarcodes") |
| 1666 | (version "1.14.0") |
| 1667 | (source |
| 1668 | (origin |
| 1669 | (method url-fetch) |
| 1670 | (uri (bioconductor-uri "DNABarcodes" version)) |
| 1671 | (sha256 |
| 1672 | (base32 |
| 1673 | "1a0c9ag9n41cs0da9lfvpkxf7n5vbrfypaygdv66mw73aibix6v0")))) |
| 1674 | (properties `((upstream-name . "DNABarcodes"))) |
| 1675 | (build-system r-build-system) |
| 1676 | (propagated-inputs |
| 1677 | `(("r-bh" ,r-bh) |
| 1678 | ("r-matrix" ,r-matrix) |
| 1679 | ("r-rcpp" ,r-rcpp))) |
| 1680 | (home-page "https://bioconductor.org/packages/DNABarcodes") |
| 1681 | (synopsis "Create and analyze DNA barcodes") |
| 1682 | (description |
| 1683 | "This package offers tools to create DNA barcode sets capable of |
| 1684 | correcting insertion, deletion, and substitution errors. Existing barcodes |
| 1685 | can be analyzed regarding their minimal, maximal and average distances between |
| 1686 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be |
| 1687 | demultiplexed, i.e. assigned to their original reference barcode.") |
| 1688 | (license license:gpl2))) |
| 1689 | |
| 1690 | (define-public r-ruvseq |
| 1691 | (package |
| 1692 | (name "r-ruvseq") |
| 1693 | (version "1.18.0") |
| 1694 | (source |
| 1695 | (origin |
| 1696 | (method url-fetch) |
| 1697 | (uri (bioconductor-uri "RUVSeq" version)) |
| 1698 | (sha256 |
| 1699 | (base32 |
| 1700 | "0ln4qc9d5r15zlhazx6annx97c0wrx3jqpcvk7yj1jnwh349lw33")))) |
| 1701 | (properties `((upstream-name . "RUVSeq"))) |
| 1702 | (build-system r-build-system) |
| 1703 | (propagated-inputs |
| 1704 | `(("r-biobase" ,r-biobase) |
| 1705 | ("r-edaseq" ,r-edaseq) |
| 1706 | ("r-edger" ,r-edger) |
| 1707 | ("r-mass" ,r-mass))) |
| 1708 | (home-page "https://github.com/drisso/RUVSeq") |
| 1709 | (synopsis "Remove unwanted variation from RNA-Seq data") |
| 1710 | (description |
| 1711 | "This package implements methods to @dfn{remove unwanted variation} (RUV) |
| 1712 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between |
| 1713 | samples.") |
| 1714 | (license license:artistic2.0))) |
| 1715 | |
| 1716 | (define-public r-biocneighbors |
| 1717 | (package |
| 1718 | (name "r-biocneighbors") |
| 1719 | (version "1.2.0") |
| 1720 | (source |
| 1721 | (origin |
| 1722 | (method url-fetch) |
| 1723 | (uri (bioconductor-uri "BiocNeighbors" version)) |
| 1724 | (sha256 |
| 1725 | (base32 |
| 1726 | "08ak72y6mafzkhzfkx6b7waljpa0f1nxcrvyspd88sgzxgxjnkmg")))) |
| 1727 | (properties `((upstream-name . "BiocNeighbors"))) |
| 1728 | (build-system r-build-system) |
| 1729 | (propagated-inputs |
| 1730 | `(("r-biocgenerics" ,r-biocgenerics) |
| 1731 | ("r-biocparallel" ,r-biocparallel) |
| 1732 | ("r-rcpp" ,r-rcpp) |
| 1733 | ("r-rcppannoy" ,r-rcppannoy) |
| 1734 | ("r-rcpphnsw" ,r-rcpphnsw) |
| 1735 | ("r-s4vectors" ,r-s4vectors))) |
| 1736 | (home-page "https://bioconductor.org/packages/BiocNeighbors") |
| 1737 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") |
| 1738 | (description |
| 1739 | "This package implements exact and approximate methods for nearest |
| 1740 | neighbor detection, in a framework that allows them to be easily switched |
| 1741 | within Bioconductor packages or workflows. The exact algorithm is implemented |
| 1742 | using pre-clustering with the k-means algorithm. Functions are also provided |
| 1743 | to search for all neighbors within a given distance. Parallelization is |
| 1744 | achieved for all methods using the BiocParallel framework.") |
| 1745 | (license license:gpl3))) |
| 1746 | |
| 1747 | (define-public r-biocsingular |
| 1748 | (package |
| 1749 | (name "r-biocsingular") |
| 1750 | (version "1.0.0") |
| 1751 | (source |
| 1752 | (origin |
| 1753 | (method url-fetch) |
| 1754 | (uri (bioconductor-uri "BiocSingular" version)) |
| 1755 | (sha256 |
| 1756 | (base32 |
| 1757 | "129z6bkdhm5wlvrjiwrr8yl2jj9chh4i6dm6firlj4c4ql3jp4f5")))) |
| 1758 | (properties `((upstream-name . "BiocSingular"))) |
| 1759 | (build-system r-build-system) |
| 1760 | (propagated-inputs |
| 1761 | `(("r-beachmat" ,r-beachmat) |
| 1762 | ("r-biocgenerics" ,r-biocgenerics) |
| 1763 | ("r-biocparallel" ,r-biocparallel) |
| 1764 | ("r-delayedarray" ,r-delayedarray) |
| 1765 | ("r-irlba" ,r-irlba) |
| 1766 | ("r-matrix" ,r-matrix) |
| 1767 | ("r-rcpp" ,r-rcpp) |
| 1768 | ("r-rsvd" ,r-rsvd) |
| 1769 | ("r-s4vectors" ,r-s4vectors))) |
| 1770 | (home-page "https://github.com/LTLA/BiocSingular") |
| 1771 | (synopsis "Singular value decomposition for Bioconductor packages") |
| 1772 | (description |
| 1773 | "This package implements exact and approximate methods for singular value |
| 1774 | decomposition and principal components analysis, in a framework that allows |
| 1775 | them to be easily switched within Bioconductor packages or workflows. Where |
| 1776 | possible, parallelization is achieved using the BiocParallel framework.") |
| 1777 | (license license:gpl3))) |
| 1778 | |
| 1779 | (define-public r-destiny |
| 1780 | (package |
| 1781 | (name "r-destiny") |
| 1782 | (version "2.14.0") |
| 1783 | (source |
| 1784 | (origin |
| 1785 | (method url-fetch) |
| 1786 | (uri (bioconductor-uri "destiny" version)) |
| 1787 | (sha256 |
| 1788 | (base32 |
| 1789 | "1bpa114fgrknn6415g4d1jrvb924nkwi18jzfqribpvcf1vlgrf3")))) |
| 1790 | (build-system r-build-system) |
| 1791 | (propagated-inputs |
| 1792 | `(("r-biobase" ,r-biobase) |
| 1793 | ("r-biocgenerics" ,r-biocgenerics) |
| 1794 | ("r-ggplot2" ,r-ggplot2) |
| 1795 | ("r-ggthemes" ,r-ggthemes) |
| 1796 | ("r-igraph" ,r-igraph) |
| 1797 | ("r-matrix" ,r-matrix) |
| 1798 | ("r-proxy" ,r-proxy) |
| 1799 | ("r-rcpp" ,r-rcpp) |
| 1800 | ("r-rcppeigen" ,r-rcppeigen) |
| 1801 | ("r-scales" ,r-scales) |
| 1802 | ("r-scatterplot3d" ,r-scatterplot3d) |
| 1803 | ("r-smoother" ,r-smoother) |
| 1804 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 1805 | ("r-vim" ,r-vim))) |
| 1806 | (home-page "https://bioconductor.org/packages/destiny/") |
| 1807 | (synopsis "Create and plot diffusion maps") |
| 1808 | (description "This package provides tools to create and plot diffusion |
| 1809 | maps.") |
| 1810 | ;; Any version of the GPL |
| 1811 | (license license:gpl3+))) |
| 1812 | |
| 1813 | (define-public r-savr |
| 1814 | (package |
| 1815 | (name "r-savr") |
| 1816 | (version "1.22.0") |
| 1817 | (source |
| 1818 | (origin |
| 1819 | (method url-fetch) |
| 1820 | (uri (bioconductor-uri "savR" version)) |
| 1821 | (sha256 |
| 1822 | (base32 |
| 1823 | "101p0c07p49c50lfnbfanyyikdypmqkvwclqifq32js9phqwhf6h")))) |
| 1824 | (properties `((upstream-name . "savR"))) |
| 1825 | (build-system r-build-system) |
| 1826 | (propagated-inputs |
| 1827 | `(("r-ggplot2" ,r-ggplot2) |
| 1828 | ("r-gridextra" ,r-gridextra) |
| 1829 | ("r-reshape2" ,r-reshape2) |
| 1830 | ("r-scales" ,r-scales) |
| 1831 | ("r-xml" ,r-xml))) |
| 1832 | (home-page "https://github.com/bcalder/savR") |
| 1833 | (synopsis "Parse and analyze Illumina SAV files") |
| 1834 | (description |
| 1835 | "This package provides tools to parse Illumina Sequence Analysis |
| 1836 | Viewer (SAV) files, access data, and generate QC plots.") |
| 1837 | (license license:agpl3+))) |
| 1838 | |
| 1839 | (define-public r-chipexoqual |
| 1840 | (package |
| 1841 | (name "r-chipexoqual") |
| 1842 | (version "1.8.0") |
| 1843 | (source |
| 1844 | (origin |
| 1845 | (method url-fetch) |
| 1846 | (uri (bioconductor-uri "ChIPexoQual" version)) |
| 1847 | (sha256 |
| 1848 | (base32 |
| 1849 | "02341i3lg74czgapf5qc6zvi2321af3rp85qavbg209fyc219acj")))) |
| 1850 | (properties `((upstream-name . "ChIPexoQual"))) |
| 1851 | (build-system r-build-system) |
| 1852 | (propagated-inputs |
| 1853 | `(("r-biocparallel" ,r-biocparallel) |
| 1854 | ("r-biovizbase" ,r-biovizbase) |
| 1855 | ("r-broom" ,r-broom) |
| 1856 | ("r-data-table" ,r-data-table) |
| 1857 | ("r-dplyr" ,r-dplyr) |
| 1858 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1859 | ("r-genomicalignments" ,r-genomicalignments) |
| 1860 | ("r-genomicranges" ,r-genomicranges) |
| 1861 | ("r-ggplot2" ,r-ggplot2) |
| 1862 | ("r-hexbin" ,r-hexbin) |
| 1863 | ("r-iranges" ,r-iranges) |
| 1864 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 1865 | ("r-rmarkdown" ,r-rmarkdown) |
| 1866 | ("r-rsamtools" ,r-rsamtools) |
| 1867 | ("r-s4vectors" ,r-s4vectors) |
| 1868 | ("r-scales" ,r-scales) |
| 1869 | ("r-viridis" ,r-viridis))) |
| 1870 | (home-page "https://github.com/keleslab/ChIPexoQual") |
| 1871 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") |
| 1872 | (description |
| 1873 | "This package provides a quality control pipeline for ChIP-exo/nexus |
| 1874 | sequencing data.") |
| 1875 | (license license:gpl2+))) |
| 1876 | |
| 1877 | (define-public r-copynumber |
| 1878 | (package |
| 1879 | (name "r-copynumber") |
| 1880 | (version "1.24.0") |
| 1881 | (source (origin |
| 1882 | (method url-fetch) |
| 1883 | (uri (bioconductor-uri "copynumber" version)) |
| 1884 | (sha256 |
| 1885 | (base32 |
| 1886 | "0gmxi7w776pjqv3v0pkdihb167zzrnr9hw64yfvzgjhkhrc6a4rp")))) |
| 1887 | (build-system r-build-system) |
| 1888 | (propagated-inputs |
| 1889 | `(("r-s4vectors" ,r-s4vectors) |
| 1890 | ("r-iranges" ,r-iranges) |
| 1891 | ("r-genomicranges" ,r-genomicranges) |
| 1892 | ("r-biocgenerics" ,r-biocgenerics))) |
| 1893 | (home-page "https://bioconductor.org/packages/copynumber") |
| 1894 | (synopsis "Segmentation of single- and multi-track copy number data") |
| 1895 | (description |
| 1896 | "This package segments single- and multi-track copy number data by a |
| 1897 | penalized least squares regression method.") |
| 1898 | (license license:artistic2.0))) |
| 1899 | |
| 1900 | (define-public r-dnacopy |
| 1901 | (package |
| 1902 | (name "r-dnacopy") |
| 1903 | (version "1.58.0") |
| 1904 | (source |
| 1905 | (origin |
| 1906 | (method url-fetch) |
| 1907 | (uri (bioconductor-uri "DNAcopy" version)) |
| 1908 | (sha256 |
| 1909 | (base32 |
| 1910 | "1gybr3cbsrqjgz00n4l5kb2nrmh302xpvzk5zk957ijj5qbfwmxa")))) |
| 1911 | (properties `((upstream-name . "DNAcopy"))) |
| 1912 | (build-system r-build-system) |
| 1913 | (native-inputs `(("gfortran" ,gfortran))) |
| 1914 | (home-page "https://bioconductor.org/packages/DNAcopy") |
| 1915 | (synopsis "DNA copy number data analysis") |
| 1916 | (description |
| 1917 | "This package implements the @dfn{circular binary segmentation} (CBS) |
| 1918 | algorithm to segment DNA copy number data and identify genomic regions with |
| 1919 | abnormal copy number.") |
| 1920 | (license license:gpl2+))) |
| 1921 | |
| 1922 | ;; This is a CRAN package, but it uncharacteristically depends on a |
| 1923 | ;; Bioconductor package. |
| 1924 | (define-public r-htscluster |
| 1925 | (package |
| 1926 | (name "r-htscluster") |
| 1927 | (version "2.0.8") |
| 1928 | (source |
| 1929 | (origin |
| 1930 | (method url-fetch) |
| 1931 | (uri (cran-uri "HTSCluster" version)) |
| 1932 | (sha256 |
| 1933 | (base32 |
| 1934 | "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg")))) |
| 1935 | (properties `((upstream-name . "HTSCluster"))) |
| 1936 | (build-system r-build-system) |
| 1937 | (propagated-inputs |
| 1938 | `(("r-capushe" ,r-capushe) |
| 1939 | ("r-edger" ,r-edger) |
| 1940 | ("r-plotrix" ,r-plotrix))) |
| 1941 | (home-page "https://cran.r-project.org/web/packages/HTSCluster") |
| 1942 | (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data") |
| 1943 | (description |
| 1944 | "This package provides a Poisson mixture model is implemented to cluster |
| 1945 | genes from high-throughput transcriptome sequencing (RNA-seq) data. Parameter |
| 1946 | estimation is performed using either the EM or CEM algorithm, and the slope |
| 1947 | heuristics are used for model selection (i.e., to choose the number of |
| 1948 | clusters).") |
| 1949 | (license license:gpl3+))) |
| 1950 | |
| 1951 | (define-public r-deds |
| 1952 | (package |
| 1953 | (name "r-deds") |
| 1954 | (version "1.58.0") |
| 1955 | (source |
| 1956 | (origin |
| 1957 | (method url-fetch) |
| 1958 | (uri (bioconductor-uri "DEDS" version)) |
| 1959 | (sha256 |
| 1960 | (base32 |
| 1961 | "029g7wgxc7yp1cdyalbi8gipkskrgp7nyl1s2whhjy5dqpfcpigs")))) |
| 1962 | (properties `((upstream-name . "DEDS"))) |
| 1963 | (build-system r-build-system) |
| 1964 | (home-page "https://bioconductor.org/packages/DEDS/") |
| 1965 | (synopsis "Differential expression via distance summary for microarray data") |
| 1966 | (description |
| 1967 | "This library contains functions that calculate various statistics of |
| 1968 | differential expression for microarray data, including t statistics, fold |
| 1969 | change, F statistics, SAM, moderated t and F statistics and B statistics. It |
| 1970 | also implements a new methodology called DEDS (Differential Expression via |
| 1971 | Distance Summary), which selects differentially expressed genes by integrating |
| 1972 | and summarizing a set of statistics using a weighted distance approach.") |
| 1973 | ;; Any version of the LGPL. |
| 1974 | (license license:lgpl3+))) |
| 1975 | |
| 1976 | ;; This is a CRAN package, but since it depends on a Bioconductor package we |
| 1977 | ;; put it here. |
| 1978 | (define-public r-nbpseq |
| 1979 | (package |
| 1980 | (name "r-nbpseq") |
| 1981 | (version "0.3.0") |
| 1982 | (source |
| 1983 | (origin |
| 1984 | (method url-fetch) |
| 1985 | (uri (cran-uri "NBPSeq" version)) |
| 1986 | (sha256 |
| 1987 | (base32 |
| 1988 | "0l4ylxhs2k9ww21jjqs67fygk92avdchhx2y1ixzl7yr2yh1y9by")))) |
| 1989 | (properties `((upstream-name . "NBPSeq"))) |
| 1990 | (build-system r-build-system) |
| 1991 | (propagated-inputs |
| 1992 | `(("r-qvalue" ,r-qvalue))) |
| 1993 | (home-page "https://cran.r-project.org/web/packages/NBPSeq") |
| 1994 | (synopsis "Negative binomial models for RNA-Seq data") |
| 1995 | (description |
| 1996 | "This package provides negative binomial models for two-group comparisons |
| 1997 | and regression inferences from RNA-sequencing data.") |
| 1998 | (license license:gpl2))) |
| 1999 | |
| 2000 | (define-public r-ebseq |
| 2001 | (package |
| 2002 | (name "r-ebseq") |
| 2003 | (version "1.24.0") |
| 2004 | (source |
| 2005 | (origin |
| 2006 | (method url-fetch) |
| 2007 | (uri (bioconductor-uri "EBSeq" version)) |
| 2008 | (sha256 |
| 2009 | (base32 |
| 2010 | "13rf85gffqn86r5gqibla3gqrnnag2zinrfawpcsgn3fk7hl3v83")))) |
| 2011 | (properties `((upstream-name . "EBSeq"))) |
| 2012 | (build-system r-build-system) |
| 2013 | (propagated-inputs |
| 2014 | `(("r-blockmodeling" ,r-blockmodeling) |
| 2015 | ("r-gplots" ,r-gplots) |
| 2016 | ("r-testthat" ,r-testthat))) |
| 2017 | (home-page "https://bioconductor.org/packages/EBSeq") |
| 2018 | (synopsis "Differential expression analysis of RNA-seq data") |
| 2019 | (description |
| 2020 | "This package provides tools for differential expression analysis at both |
| 2021 | gene and isoform level using RNA-seq data") |
| 2022 | (license license:artistic2.0))) |
| 2023 | |
| 2024 | (define-public r-lpsymphony |
| 2025 | (package |
| 2026 | (name "r-lpsymphony") |
| 2027 | (version "1.12.0") |
| 2028 | (source |
| 2029 | (origin |
| 2030 | (method url-fetch) |
| 2031 | (uri (bioconductor-uri "lpsymphony" version)) |
| 2032 | (sha256 |
| 2033 | (base32 |
| 2034 | "13wvq4ip8nkyxmpncs6fzcf3vphra1n0fd5vz9kspbch0k1z6bsv")))) |
| 2035 | (build-system r-build-system) |
| 2036 | (inputs |
| 2037 | `(("gfortran" ,gfortran) |
| 2038 | ("zlib" ,zlib))) |
| 2039 | (native-inputs |
| 2040 | `(("pkg-config" ,pkg-config))) |
| 2041 | (home-page "http://r-forge.r-project.org/projects/rsymphony") |
| 2042 | (synopsis "Symphony integer linear programming solver in R") |
| 2043 | (description |
| 2044 | "This package was derived from Rsymphony. The package provides an R |
| 2045 | interface to SYMPHONY, a linear programming solver written in C++. The main |
| 2046 | difference between this package and Rsymphony is that it includes the solver |
| 2047 | source code, while Rsymphony expects to find header and library files on the |
| 2048 | users' system. Thus the intention of @code{lpsymphony} is to provide an easy |
| 2049 | to install interface to SYMPHONY.") |
| 2050 | ;; Symphony 5.4 or later is distributed under the terms of the EPL 1.0. |
| 2051 | ;; lpsimphony is released under the same terms. |
| 2052 | (license license:epl1.0))) |
| 2053 | |
| 2054 | (define-public r-ihw |
| 2055 | (package |
| 2056 | (name "r-ihw") |
| 2057 | (version "1.12.0") |
| 2058 | (source |
| 2059 | (origin |
| 2060 | (method url-fetch) |
| 2061 | (uri (bioconductor-uri "IHW" version)) |
| 2062 | (sha256 |
| 2063 | (base32 |
| 2064 | "05hs6w1albkbyqzkid0bchb5zs41f31a7vhfbcswryhc86cxwzkz")))) |
| 2065 | (properties `((upstream-name . "IHW"))) |
| 2066 | (build-system r-build-system) |
| 2067 | (propagated-inputs |
| 2068 | `(("r-biocgenerics" ,r-biocgenerics) |
| 2069 | ("r-fdrtool" ,r-fdrtool) |
| 2070 | ("r-lpsymphony" ,r-lpsymphony) |
| 2071 | ("r-slam" ,r-slam))) |
| 2072 | (home-page "https://bioconductor.org/packages/IHW") |
| 2073 | (synopsis "Independent hypothesis weighting") |
| 2074 | (description |
| 2075 | "@dfn{Independent hypothesis weighting} (IHW) is a multiple testing |
| 2076 | procedure that increases power compared to the method of Benjamini and |
| 2077 | Hochberg by assigning data-driven weights to each hypothesis. The input to |
| 2078 | IHW is a two-column table of p-values and covariates. The covariate can be |
| 2079 | any continuous-valued or categorical variable that is thought to be |
| 2080 | informative on the statistical properties of each hypothesis test, while it is |
| 2081 | independent of the p-value under the null hypothesis.") |
| 2082 | (license license:artistic2.0))) |
| 2083 | |
| 2084 | (define-public r-icobra |
| 2085 | (package |
| 2086 | (name "r-icobra") |
| 2087 | (version "1.12.0") |
| 2088 | (source |
| 2089 | (origin |
| 2090 | (method url-fetch) |
| 2091 | (uri (bioconductor-uri "iCOBRA" version)) |
| 2092 | (sha256 |
| 2093 | (base32 |
| 2094 | "1w9frnczgypzc2czbwrvlizqcqhbp6cdpyws7vkmnn9k0ggzxvfc")))) |
| 2095 | (properties `((upstream-name . "iCOBRA"))) |
| 2096 | (build-system r-build-system) |
| 2097 | (propagated-inputs |
| 2098 | `(("r-dplyr" ,r-dplyr) |
| 2099 | ("r-dt" ,r-dt) |
| 2100 | ("r-ggplot2" ,r-ggplot2) |
| 2101 | ("r-limma" ,r-limma) |
| 2102 | ("r-reshape2" ,r-reshape2) |
| 2103 | ("r-rocr" ,r-rocr) |
| 2104 | ("r-scales" ,r-scales) |
| 2105 | ("r-shiny" ,r-shiny) |
| 2106 | ("r-shinybs" ,r-shinybs) |
| 2107 | ("r-shinydashboard" ,r-shinydashboard) |
| 2108 | ("r-upsetr" ,r-upsetr))) |
| 2109 | (home-page "https://bioconductor.org/packages/iCOBRA") |
| 2110 | (synopsis "Comparison and visualization of ranking and assignment methods") |
| 2111 | (description |
| 2112 | "This package provides functions for calculation and visualization of |
| 2113 | performance metrics for evaluation of ranking and binary |
| 2114 | classification (assignment) methods. It also contains a Shiny application for |
| 2115 | interactive exploration of results.") |
| 2116 | (license license:gpl2+))) |
| 2117 | |
| 2118 | (define-public r-mast |
| 2119 | (package |
| 2120 | (name "r-mast") |
| 2121 | (version "1.10.0") |
| 2122 | (source |
| 2123 | (origin |
| 2124 | (method url-fetch) |
| 2125 | (uri (bioconductor-uri "MAST" version)) |
| 2126 | (sha256 |
| 2127 | (base32 |
| 2128 | "0f2qkp346095k9m45frpd3bivrvaps9wlm0m3n0z8j0aj7w1kqlx")))) |
| 2129 | (properties `((upstream-name . "MAST"))) |
| 2130 | (build-system r-build-system) |
| 2131 | (propagated-inputs |
| 2132 | `(("r-abind" ,r-abind) |
| 2133 | ("r-blme" ,r-blme) |
| 2134 | ("r-biobase" ,r-biobase) |
| 2135 | ("r-biocgenerics" ,r-biocgenerics) |
| 2136 | ("r-data-table" ,r-data-table) |
| 2137 | ("r-ggplot2" ,r-ggplot2) |
| 2138 | ("r-plyr" ,r-plyr) |
| 2139 | ("r-progress" ,r-progress) |
| 2140 | ("r-reshape2" ,r-reshape2) |
| 2141 | ("r-s4vectors" ,r-s4vectors) |
| 2142 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
| 2143 | ("r-stringr" ,r-stringr) |
| 2144 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 2145 | (home-page "https://github.com/RGLab/MAST/") |
| 2146 | (synopsis "Model-based analysis of single cell transcriptomics") |
| 2147 | (description |
| 2148 | "This package provides methods and models for handling zero-inflated |
| 2149 | single cell assay data.") |
| 2150 | (license license:gpl2+))) |
| 2151 | |
| 2152 | (define-public r-monocle |
| 2153 | (package |
| 2154 | (name "r-monocle") |
| 2155 | (version "2.12.0") |
| 2156 | (source |
| 2157 | (origin |
| 2158 | (method url-fetch) |
| 2159 | (uri (bioconductor-uri "monocle" version)) |
| 2160 | (sha256 |
| 2161 | (base32 |
| 2162 | "1rnr3k0wc61a806w9flapni91wz5xm0l66jabjzx0vbiwgczs32z")))) |
| 2163 | (build-system r-build-system) |
| 2164 | (propagated-inputs |
| 2165 | `(("r-biobase" ,r-biobase) |
| 2166 | ("r-biocgenerics" ,r-biocgenerics) |
| 2167 | ("r-biocviews" ,r-biocviews) |
| 2168 | ("r-cluster" ,r-cluster) |
| 2169 | ("r-combinat" ,r-combinat) |
| 2170 | ("r-ddrtree" ,r-ddrtree) |
| 2171 | ("r-densityclust" ,r-densityclust) |
| 2172 | ("r-dplyr" ,r-dplyr) |
| 2173 | ("r-fastica" ,r-fastica) |
| 2174 | ("r-ggplot2" ,r-ggplot2) |
| 2175 | ("r-hsmmsinglecell" ,r-hsmmsinglecell) |
| 2176 | ("r-igraph" ,r-igraph) |
| 2177 | ("r-irlba" ,r-irlba) |
| 2178 | ("r-limma" ,r-limma) |
| 2179 | ("r-mass" ,r-mass) |
| 2180 | ("r-matrix" ,r-matrix) |
| 2181 | ("r-matrixstats" ,r-matrixstats) |
| 2182 | ("r-pheatmap" ,r-pheatmap) |
| 2183 | ("r-plyr" ,r-plyr) |
| 2184 | ("r-proxy" ,r-proxy) |
| 2185 | ("r-qlcmatrix" ,r-qlcmatrix) |
| 2186 | ("r-rann" ,r-rann) |
| 2187 | ("r-rcpp" ,r-rcpp) |
| 2188 | ("r-reshape2" ,r-reshape2) |
| 2189 | ("r-rtsne" ,r-rtsne) |
| 2190 | ("r-slam" ,r-slam) |
| 2191 | ("r-stringr" ,r-stringr) |
| 2192 | ("r-tibble" ,r-tibble) |
| 2193 | ("r-vgam" ,r-vgam) |
| 2194 | ("r-viridis" ,r-viridis))) |
| 2195 | (home-page "https://bioconductor.org/packages/monocle") |
| 2196 | (synopsis "Clustering, differential expression, and trajectory analysis for single-cell RNA-Seq") |
| 2197 | (description |
| 2198 | "Monocle performs differential expression and time-series analysis for |
| 2199 | single-cell expression experiments. It orders individual cells according to |
| 2200 | progress through a biological process, without knowing ahead of time which |
| 2201 | genes define progress through that process. Monocle also performs |
| 2202 | differential expression analysis, clustering, visualization, and other useful |
| 2203 | tasks on single cell expression data. It is designed to work with RNA-Seq and |
| 2204 | qPCR data, but could be used with other types as well.") |
| 2205 | (license license:artistic2.0))) |
| 2206 | |
| 2207 | (define-public r-noiseq |
| 2208 | (package |
| 2209 | (name "r-noiseq") |
| 2210 | (version "2.28.0") |
| 2211 | (source |
| 2212 | (origin |
| 2213 | (method url-fetch) |
| 2214 | (uri (bioconductor-uri "NOISeq" version)) |
| 2215 | (sha256 |
| 2216 | (base32 |
| 2217 | "1k7k0xqa0lxj6mfsvbmd6x6glv9wynbwl87w5d3bilbq4dpc139j")))) |
| 2218 | (properties `((upstream-name . "NOISeq"))) |
| 2219 | (build-system r-build-system) |
| 2220 | (propagated-inputs |
| 2221 | `(("r-biobase" ,r-biobase) |
| 2222 | ("r-matrix" ,r-matrix))) |
| 2223 | (home-page "https://bioconductor.org/packages/NOISeq") |
| 2224 | (synopsis "Exploratory analysis and differential expression for RNA-seq data") |
| 2225 | (description |
| 2226 | "This package provides tools to support the analysis of RNA-seq |
| 2227 | expression data or other similar kind of data. It provides exploratory plots |
| 2228 | to evaluate saturation, count distribution, expression per chromosome, type of |
| 2229 | detected features, features length, etc. It also supports the analysis of |
| 2230 | differential expression between two experimental conditions with no parametric |
| 2231 | assumptions.") |
| 2232 | (license license:artistic2.0))) |
| 2233 | |
| 2234 | (define-public r-scdd |
| 2235 | (package |
| 2236 | (name "r-scdd") |
| 2237 | (version "1.8.0") |
| 2238 | (source |
| 2239 | (origin |
| 2240 | (method url-fetch) |
| 2241 | (uri (bioconductor-uri "scDD" version)) |
| 2242 | (sha256 |
| 2243 | (base32 |
| 2244 | "01hp6xxxap7541yi5dv596xvamqyyihvgkdy224ixa0n2cxyrhyf")))) |
| 2245 | (properties `((upstream-name . "scDD"))) |
| 2246 | (build-system r-build-system) |
| 2247 | (propagated-inputs |
| 2248 | `(("r-arm" ,r-arm) |
| 2249 | ("r-biocparallel" ,r-biocparallel) |
| 2250 | ("r-ebseq" ,r-ebseq) |
| 2251 | ("r-fields" ,r-fields) |
| 2252 | ("r-ggplot2" ,r-ggplot2) |
| 2253 | ("r-mclust" ,r-mclust) |
| 2254 | ("r-outliers" ,r-outliers) |
| 2255 | ("r-s4vectors" ,r-s4vectors) |
| 2256 | ("r-scran" ,r-scran) |
| 2257 | ("r-singlecellexperiment" ,r-singlecellexperiment) |
| 2258 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 2259 | (home-page "https://github.com/kdkorthauer/scDD") |
| 2260 | (synopsis "Mixture modeling of single-cell RNA-seq data") |
| 2261 | (description |
| 2262 | "This package implements a method to analyze single-cell RNA-seq data |
| 2263 | utilizing flexible Dirichlet Process mixture models. Genes with differential |
| 2264 | distributions of expression are classified into several interesting patterns |
| 2265 | of differences between two conditions. The package also includes functions |
| 2266 | for simulating data with these patterns from negative binomial |
| 2267 | distributions.") |
| 2268 | (license license:gpl2))) |
| 2269 | |
| 2270 | (define-public r-scone |
| 2271 | (package |
| 2272 | (name "r-scone") |
| 2273 | (version "1.8.0") |
| 2274 | (source |
| 2275 | (origin |
| 2276 | (method url-fetch) |
| 2277 | (uri (bioconductor-uri "scone" version)) |
| 2278 | (sha256 |
| 2279 | (base32 |
| 2280 | "00cr0jp1ywxygf2pryw7mmcmn7cp1500fvifkbwgg2qxbkq5zqck")))) |
| 2281 | (build-system r-build-system) |
| 2282 | (propagated-inputs |
| 2283 | `(("r-aroma-light" ,r-aroma-light) |
| 2284 | ("r-biocparallel" ,r-biocparallel) |
| 2285 | ("r-boot" ,r-boot) |
| 2286 | ("r-class" ,r-class) |
| 2287 | ("r-cluster" ,r-cluster) |
| 2288 | ("r-compositions" ,r-compositions) |
| 2289 | ("r-diptest" ,r-diptest) |
| 2290 | ("r-edger" ,r-edger) |
| 2291 | ("r-fpc" ,r-fpc) |
| 2292 | ("r-gplots" ,r-gplots) |
| 2293 | ("r-hexbin" ,r-hexbin) |
| 2294 | ("r-limma" ,r-limma) |
| 2295 | ("r-matrixstats" ,r-matrixstats) |
| 2296 | ("r-mixtools" ,r-mixtools) |
| 2297 | ("r-rarpack" ,r-rarpack) |
| 2298 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 2299 | ("r-rhdf5" ,r-rhdf5) |
| 2300 | ("r-ruvseq" ,r-ruvseq) |
| 2301 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 2302 | (home-page "https://bioconductor.org/packages/scone") |
| 2303 | (synopsis "Single cell overview of normalized expression data") |
| 2304 | (description |
| 2305 | "SCONE is an R package for comparing and ranking the performance of |
| 2306 | different normalization schemes for single-cell RNA-seq and other |
| 2307 | high-throughput analyses.") |
| 2308 | (license license:artistic2.0))) |
| 2309 | |
| 2310 | (define-public r-geoquery |
| 2311 | (package |
| 2312 | (name "r-geoquery") |
| 2313 | (version "2.52.0") |
| 2314 | (source |
| 2315 | (origin |
| 2316 | (method url-fetch) |
| 2317 | (uri (bioconductor-uri "GEOquery" version)) |
| 2318 | (sha256 |
| 2319 | (base32 |
| 2320 | "1r8x4jsl1mr9j7wyyqlj0zgwd80vkqhxxqrcgbb78ksryzq45jkr")))) |
| 2321 | (properties `((upstream-name . "GEOquery"))) |
| 2322 | (build-system r-build-system) |
| 2323 | (propagated-inputs |
| 2324 | `(("r-biobase" ,r-biobase) |
| 2325 | ("r-dplyr" ,r-dplyr) |
| 2326 | ("r-httr" ,r-httr) |
| 2327 | ("r-limma" ,r-limma) |
| 2328 | ("r-magrittr" ,r-magrittr) |
| 2329 | ("r-readr" ,r-readr) |
| 2330 | ("r-tidyr" ,r-tidyr) |
| 2331 | ("r-xml2" ,r-xml2))) |
| 2332 | (home-page "https://github.com/seandavi/GEOquery/") |
| 2333 | (synopsis "Get data from NCBI Gene Expression Omnibus (GEO)") |
| 2334 | (description |
| 2335 | "The NCBI Gene Expression Omnibus (GEO) is a public repository of |
| 2336 | microarray data. Given the rich and varied nature of this resource, it is |
| 2337 | only natural to want to apply BioConductor tools to these data. GEOquery is |
| 2338 | the bridge between GEO and BioConductor.") |
| 2339 | (license license:gpl2))) |
| 2340 | |
| 2341 | (define-public r-illuminaio |
| 2342 | (package |
| 2343 | (name "r-illuminaio") |
| 2344 | (version "0.26.0") |
| 2345 | (source |
| 2346 | (origin |
| 2347 | (method url-fetch) |
| 2348 | (uri (bioconductor-uri "illuminaio" version)) |
| 2349 | (sha256 |
| 2350 | (base32 |
| 2351 | "18plm8p40gfzfmqflxssrdj8az3xvmnmh9i9dafl3af3bxwv03l8")))) |
| 2352 | (build-system r-build-system) |
| 2353 | (propagated-inputs |
| 2354 | `(("r-base64" ,r-base64))) |
| 2355 | (home-page "https://github.com/HenrikBengtsson/illuminaio/") |
| 2356 | (synopsis "Parse Illumina microarray output files") |
| 2357 | (description |
| 2358 | "This package provides tools for parsing Illumina's microarray output |
| 2359 | files, including IDAT.") |
| 2360 | (license license:gpl2))) |
| 2361 | |
| 2362 | (define-public r-siggenes |
| 2363 | (package |
| 2364 | (name "r-siggenes") |
| 2365 | (version "1.58.0") |
| 2366 | (source |
| 2367 | (origin |
| 2368 | (method url-fetch) |
| 2369 | (uri (bioconductor-uri "siggenes" version)) |
| 2370 | (sha256 |
| 2371 | (base32 |
| 2372 | "178jmmdxsv3rd71a9w5yrvg5aplak40hb42vna15g1d55c2yv1ib")))) |
| 2373 | (build-system r-build-system) |
| 2374 | (propagated-inputs |
| 2375 | `(("r-biobase" ,r-biobase) |
| 2376 | ("r-multtest" ,r-multtest) |
| 2377 | ("r-scrime" ,r-scrime))) |
| 2378 | (home-page "https://bioconductor.org/packages/siggenes/") |
| 2379 | (synopsis |
| 2380 | "Multiple testing using SAM and Efron's empirical Bayes approaches") |
| 2381 | (description |
| 2382 | "This package provides tools for the identification of differentially |
| 2383 | expressed genes and estimation of the @dfn{False Discovery Rate} (FDR) using |
| 2384 | both the Significance Analysis of Microarrays (SAM) and the @dfn{Empirical |
| 2385 | Bayes Analyses of Microarrays} (EBAM).") |
| 2386 | (license license:lgpl2.0+))) |
| 2387 | |
| 2388 | (define-public r-bumphunter |
| 2389 | (package |
| 2390 | (name "r-bumphunter") |
| 2391 | (version "1.26.0") |
| 2392 | (source |
| 2393 | (origin |
| 2394 | (method url-fetch) |
| 2395 | (uri (bioconductor-uri "bumphunter" version)) |
| 2396 | (sha256 |
| 2397 | (base32 |
| 2398 | "1dkyicwqdaahnxcxj6kmivkqb47yccx51lb1q0yar3xpw91vwlfx")))) |
| 2399 | (build-system r-build-system) |
| 2400 | (propagated-inputs |
| 2401 | `(("r-annotationdbi" ,r-annotationdbi) |
| 2402 | ("r-biocgenerics" ,r-biocgenerics) |
| 2403 | ("r-dorng" ,r-dorng) |
| 2404 | ("r-foreach" ,r-foreach) |
| 2405 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2406 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 2407 | ("r-genomicranges" ,r-genomicranges) |
| 2408 | ("r-iranges" ,r-iranges) |
| 2409 | ("r-iterators" ,r-iterators) |
| 2410 | ("r-limma" ,r-limma) |
| 2411 | ("r-locfit" ,r-locfit) |
| 2412 | ("r-matrixstats" ,r-matrixstats) |
| 2413 | ("r-s4vectors" ,r-s4vectors))) |
| 2414 | (home-page "https://github.com/ririzarr/bumphunter") |
| 2415 | (synopsis "Find bumps in genomic data") |
| 2416 | (description |
| 2417 | "This package provides tools for finding bumps in genomic data in order |
| 2418 | to identify differentially methylated regions in epigenetic epidemiology |
| 2419 | studies.") |
| 2420 | (license license:artistic2.0))) |
| 2421 | |
| 2422 | (define-public r-minfi |
| 2423 | (package |
| 2424 | (name "r-minfi") |
| 2425 | (version "1.30.0") |
| 2426 | (source |
| 2427 | (origin |
| 2428 | (method url-fetch) |
| 2429 | (uri (bioconductor-uri "minfi" version)) |
| 2430 | (sha256 |
| 2431 | (base32 |
| 2432 | "0qir0zd0qa97fzm33v10nyrsjp8nmzhn7mn20dnlpsg7rwlf60pd")))) |
| 2433 | (build-system r-build-system) |
| 2434 | (propagated-inputs |
| 2435 | `(("r-beanplot" ,r-beanplot) |
| 2436 | ("r-biobase" ,r-biobase) |
| 2437 | ("r-biocgenerics" ,r-biocgenerics) |
| 2438 | ("r-biocparallel" ,r-biocparallel) |
| 2439 | ("r-biostrings" ,r-biostrings) |
| 2440 | ("r-bumphunter" ,r-bumphunter) |
| 2441 | ("r-data-table" ,r-data-table) |
| 2442 | ("r-delayedarray" ,r-delayedarray) |
| 2443 | ("r-delayedmatrixstats" ,r-delayedmatrixstats) |
| 2444 | ("r-genefilter" ,r-genefilter) |
| 2445 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2446 | ("r-genomicranges" ,r-genomicranges) |
| 2447 | ("r-geoquery" ,r-geoquery) |
| 2448 | ("r-hdf5array" ,r-hdf5array) |
| 2449 | ("r-illuminaio" ,r-illuminaio) |
| 2450 | ("r-iranges" ,r-iranges) |
| 2451 | ("r-lattice" ,r-lattice) |
| 2452 | ("r-limma" ,r-limma) |
| 2453 | ("r-mass" ,r-mass) |
| 2454 | ("r-mclust" ,r-mclust) |
| 2455 | ("r-nlme" ,r-nlme) |
| 2456 | ("r-nor1mix" ,r-nor1mix) |
| 2457 | ("r-preprocesscore" ,r-preprocesscore) |
| 2458 | ("r-quadprog" ,r-quadprog) |
| 2459 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 2460 | ("r-reshape" ,r-reshape) |
| 2461 | ("r-s4vectors" ,r-s4vectors) |
| 2462 | ("r-siggenes" ,r-siggenes) |
| 2463 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 2464 | (home-page "https://github.com/hansenlab/minfi") |
| 2465 | (synopsis "Analyze Illumina Infinium DNA methylation arrays") |
| 2466 | (description |
| 2467 | "This package provides tools to analyze and visualize Illumina Infinium |
| 2468 | methylation arrays.") |
| 2469 | (license license:artistic2.0))) |
| 2470 | |
| 2471 | (define-public r-methylumi |
| 2472 | (package |
| 2473 | (name "r-methylumi") |
| 2474 | (version "2.30.0") |
| 2475 | (source |
| 2476 | (origin |
| 2477 | (method url-fetch) |
| 2478 | (uri (bioconductor-uri "methylumi" version)) |
| 2479 | (sha256 |
| 2480 | (base32 |
| 2481 | "13acn771ybi10v50x123bq5yqd62b8sr4gz77lpgaj192sxq9d9f")))) |
| 2482 | (build-system r-build-system) |
| 2483 | (propagated-inputs |
| 2484 | `(("r-annotate" ,r-annotate) |
| 2485 | ("r-annotationdbi" ,r-annotationdbi) |
| 2486 | ("r-biobase" ,r-biobase) |
| 2487 | ("r-biocgenerics" ,r-biocgenerics) |
| 2488 | ("r-fdb-infiniummethylation-hg19" ,r-fdb-infiniummethylation-hg19) |
| 2489 | ("r-genefilter" ,r-genefilter) |
| 2490 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2491 | ("r-genomicranges" ,r-genomicranges) |
| 2492 | ("r-ggplot2" ,r-ggplot2) |
| 2493 | ("r-illuminaio" ,r-illuminaio) |
| 2494 | ("r-iranges" ,r-iranges) |
| 2495 | ("r-lattice" ,r-lattice) |
| 2496 | ("r-matrixstats" ,r-matrixstats) |
| 2497 | ("r-minfi" ,r-minfi) |
| 2498 | ("r-reshape2" ,r-reshape2) |
| 2499 | ("r-s4vectors" ,r-s4vectors) |
| 2500 | ("r-scales" ,r-scales) |
| 2501 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 2502 | (home-page "https://bioconductor.org/packages/methylumi") |
| 2503 | (synopsis "Handle Illumina methylation data") |
| 2504 | (description |
| 2505 | "This package provides classes for holding and manipulating Illumina |
| 2506 | methylation data. Based on eSet, it can contain MIAME information, sample |
| 2507 | information, feature information, and multiple matrices of data. An |
| 2508 | \"intelligent\" import function, methylumiR can read the Illumina text files |
| 2509 | and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from |
| 2510 | HumanMethylation27 and HumanMethylation450 microarrays. Normalization, |
| 2511 | background correction, and quality control features for GoldenGate, Infinium, |
| 2512 | and Infinium HD arrays are also included.") |
| 2513 | (license license:gpl2))) |
| 2514 | |
| 2515 | (define-public r-lumi |
| 2516 | (package |
| 2517 | (name "r-lumi") |
| 2518 | (version "2.36.0") |
| 2519 | (source |
| 2520 | (origin |
| 2521 | (method url-fetch) |
| 2522 | (uri (bioconductor-uri "lumi" version)) |
| 2523 | (sha256 |
| 2524 | (base32 |
| 2525 | "1rf6xmd2wnajjvnl50q63agakzjf4hrzn2chdsnhapi7fh7bcjba")))) |
| 2526 | (build-system r-build-system) |
| 2527 | (propagated-inputs |
| 2528 | `(("r-affy" ,r-affy) |
| 2529 | ("r-annotate" ,r-annotate) |
| 2530 | ("r-annotationdbi" ,r-annotationdbi) |
| 2531 | ("r-biobase" ,r-biobase) |
| 2532 | ("r-dbi" ,r-dbi) |
| 2533 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 2534 | ("r-genomicranges" ,r-genomicranges) |
| 2535 | ("r-kernsmooth" ,r-kernsmooth) |
| 2536 | ("r-lattice" ,r-lattice) |
| 2537 | ("r-mass" ,r-mass) |
| 2538 | ("r-methylumi" ,r-methylumi) |
| 2539 | ("r-mgcv" ,r-mgcv) |
| 2540 | ("r-nleqslv" ,r-nleqslv) |
| 2541 | ("r-preprocesscore" ,r-preprocesscore) |
| 2542 | ("r-rsqlite" ,r-rsqlite))) |
| 2543 | (home-page "https://bioconductor.org/packages/lumi") |
| 2544 | (synopsis "BeadArray-specific methods for Illumina methylation and expression microarrays") |
| 2545 | (description |
| 2546 | "The lumi package provides an integrated solution for the Illumina |
| 2547 | microarray data analysis. It includes functions of Illumina |
| 2548 | BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific |
| 2549 | variance stabilization, normalization and gene annotation at the probe level. |
| 2550 | It also includes the functions of processing Illumina methylation microarrays, |
| 2551 | especially Illumina Infinium methylation microarrays.") |
| 2552 | (license license:lgpl2.0+))) |
| 2553 | |
| 2554 | (define-public r-linnorm |
| 2555 | (package |
| 2556 | (name "r-linnorm") |
| 2557 | (version "2.8.0") |
| 2558 | (source |
| 2559 | (origin |
| 2560 | (method url-fetch) |
| 2561 | (uri (bioconductor-uri "Linnorm" version)) |
| 2562 | (sha256 |
| 2563 | (base32 |
| 2564 | "1rv3ljdwb71364qd2p8za3jpk08agvzwas6f63s5d8wjlapzm3i5")))) |
| 2565 | (properties `((upstream-name . "Linnorm"))) |
| 2566 | (build-system r-build-system) |
| 2567 | (propagated-inputs |
| 2568 | `(("r-amap" ,r-amap) |
| 2569 | ("r-apcluster" ,r-apcluster) |
| 2570 | ("r-ellipse" ,r-ellipse) |
| 2571 | ("r-fastcluster" ,r-fastcluster) |
| 2572 | ("r-fpc" ,r-fpc) |
| 2573 | ("r-ggdendro" ,r-ggdendro) |
| 2574 | ("r-ggplot2" ,r-ggplot2) |
| 2575 | ("r-gmodels" ,r-gmodels) |
| 2576 | ("r-igraph" ,r-igraph) |
| 2577 | ("r-limma" ,r-limma) |
| 2578 | ("r-mass" ,r-mass) |
| 2579 | ("r-mclust" ,r-mclust) |
| 2580 | ("r-rcpp" ,r-rcpp) |
| 2581 | ("r-rcpparmadillo" ,r-rcpparmadillo) |
| 2582 | ("r-rtsne" ,r-rtsne) |
| 2583 | ("r-statmod" ,r-statmod) |
| 2584 | ("r-vegan" ,r-vegan) |
| 2585 | ("r-zoo" ,r-zoo))) |
| 2586 | (home-page "http://www.jjwanglab.org/Linnorm/") |
| 2587 | (synopsis "Linear model and normality based transformation method") |
| 2588 | (description |
| 2589 | "Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq |
| 2590 | count data or any large scale count data. It transforms such datasets for |
| 2591 | parametric tests. In addition to the transformtion function (@code{Linnorm}), |
| 2592 | the following pipelines are implemented: |
| 2593 | |
| 2594 | @enumerate |
| 2595 | @item Library size/batch effect normalization (@code{Linnorm.Norm}) |
| 2596 | @item Cell subpopluation analysis and visualization using t-SNE or PCA K-means |
| 2597 | clustering or hierarchical clustering (@code{Linnorm.tSNE}, |
| 2598 | @code{Linnorm.PCA}, @code{Linnorm.HClust}) |
| 2599 | @item Differential expression analysis or differential peak detection using |
| 2600 | limma (@code{Linnorm.limma}) |
| 2601 | @item Highly variable gene discovery and visualization (@code{Linnorm.HVar}) |
| 2602 | @item Gene correlation network analysis and visualization (@code{Linnorm.Cor}) |
| 2603 | @item Stable gene selection for scRNA-seq data; for users without or who do |
| 2604 | not want to rely on spike-in genes (@code{Linnorm.SGenes}) |
| 2605 | @item Data imputation (@code{Linnorm.DataImput}). |
| 2606 | @end enumerate |
| 2607 | |
| 2608 | Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the |
| 2609 | @code{RnaXSim} function is included for simulating RNA-seq data for the |
| 2610 | evaluation of DEG analysis methods.") |
| 2611 | (license license:expat))) |
| 2612 | |
| 2613 | (define-public r-ioniser |
| 2614 | (package |
| 2615 | (name "r-ioniser") |
| 2616 | (version "2.8.0") |
| 2617 | (source |
| 2618 | (origin |
| 2619 | (method url-fetch) |
| 2620 | (uri (bioconductor-uri "IONiseR" version)) |
| 2621 | (sha256 |
| 2622 | (base32 |
| 2623 | "0kznyqqpm0zbah537p197z1cgrgh9w82whmq0aydfxzgs2vxdw2y")))) |
| 2624 | (properties `((upstream-name . "IONiseR"))) |
| 2625 | (build-system r-build-system) |
| 2626 | (propagated-inputs |
| 2627 | `(("r-biocgenerics" ,r-biocgenerics) |
| 2628 | ("r-biocparallel" ,r-biocparallel) |
| 2629 | ("r-biostrings" ,r-biostrings) |
| 2630 | ("r-bit64" ,r-bit64) |
| 2631 | ("r-dplyr" ,r-dplyr) |
| 2632 | ("r-ggplot2" ,r-ggplot2) |
| 2633 | ("r-magrittr" ,r-magrittr) |
| 2634 | ("r-rhdf5" ,r-rhdf5) |
| 2635 | ("r-shortread" ,r-shortread) |
| 2636 | ("r-stringr" ,r-stringr) |
| 2637 | ("r-tibble" ,r-tibble) |
| 2638 | ("r-tidyr" ,r-tidyr) |
| 2639 | ("r-xvector" ,r-xvector))) |
| 2640 | (home-page "https://bioconductor.org/packages/IONiseR/") |
| 2641 | (synopsis "Quality assessment tools for Oxford Nanopore MinION data") |
| 2642 | (description |
| 2643 | "IONiseR provides tools for the quality assessment of Oxford Nanopore |
| 2644 | MinION data. It extracts summary statistics from a set of fast5 files and can |
| 2645 | be used either before or after base calling. In addition to standard |
| 2646 | summaries of the read-types produced, it provides a number of plots for |
| 2647 | visualising metrics relative to experiment run time or spatially over the |
| 2648 | surface of a flowcell.") |
| 2649 | (license license:expat))) |
| 2650 | |
| 2651 | ;; This is a CRAN package, but it depends on packages from Bioconductor. |
| 2652 | (define-public r-gkmsvm |
| 2653 | (package |
| 2654 | (name "r-gkmsvm") |
| 2655 | (version "0.79.0") |
| 2656 | (source |
| 2657 | (origin |
| 2658 | (method url-fetch) |
| 2659 | (uri (cran-uri "gkmSVM" version)) |
| 2660 | (sha256 |
| 2661 | (base32 |
| 2662 | "04dakbgfvfalz4rm4fvvybp506dn5fbj5g86ybfhrc6wywjllsz3")))) |
| 2663 | (properties `((upstream-name . "gkmSVM"))) |
| 2664 | (build-system r-build-system) |
| 2665 | (propagated-inputs |
| 2666 | `(("r-biocgenerics" ,r-biocgenerics) |
| 2667 | ("r-biostrings" ,r-biostrings) |
| 2668 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2669 | ("r-genomicranges" ,r-genomicranges) |
| 2670 | ("r-iranges" ,r-iranges) |
| 2671 | ("r-kernlab" ,r-kernlab) |
| 2672 | ("r-rcpp" ,r-rcpp) |
| 2673 | ("r-rocr" ,r-rocr) |
| 2674 | ("r-rtracklayer" ,r-rtracklayer) |
| 2675 | ("r-s4vectors" ,r-s4vectors) |
| 2676 | ("r-seqinr" ,r-seqinr))) |
| 2677 | (home-page "https://cran.r-project.org/web/packages/gkmSVM") |
| 2678 | (synopsis "Gapped-kmer support vector machine") |
| 2679 | (description |
| 2680 | "This R package provides tools for training gapped-kmer SVM classifiers |
| 2681 | for DNA and protein sequences. This package supports several sequence |
| 2682 | kernels, including: gkmSVM, kmer-SVM, mismatch kernel and wildcard kernel.") |
| 2683 | (license license:gpl2+))) |
| 2684 | |
| 2685 | (define-public r-triform |
| 2686 | (package |
| 2687 | (name "r-triform") |
| 2688 | (version "1.26.0") |
| 2689 | (source |
| 2690 | (origin |
| 2691 | (method url-fetch) |
| 2692 | (uri (bioconductor-uri "triform" version)) |
| 2693 | (sha256 |
| 2694 | (base32 |
| 2695 | "0bsxkn386kfx4gg19p6smy5fi3k7xdw89r5hvfsks8hsdpdz3hya")))) |
| 2696 | (build-system r-build-system) |
| 2697 | (propagated-inputs |
| 2698 | `(("r-biocgenerics" ,r-biocgenerics) |
| 2699 | ("r-iranges" ,r-iranges) |
| 2700 | ("r-yaml" ,r-yaml))) |
| 2701 | (home-page "https://bioconductor.org/packages/triform/") |
| 2702 | (synopsis "Find enriched regions in transcription factor ChIP-sequencing data") |
| 2703 | (description |
| 2704 | "The Triform algorithm uses model-free statistics to identify peak-like |
| 2705 | distributions of TF ChIP sequencing reads, taking advantage of an improved |
| 2706 | peak definition in combination with known profile characteristics.") |
| 2707 | (license license:gpl2))) |
| 2708 | |
| 2709 | (define-public r-varianttools |
| 2710 | (package |
| 2711 | (name "r-varianttools") |
| 2712 | (version "1.26.0") |
| 2713 | (source |
| 2714 | (origin |
| 2715 | (method url-fetch) |
| 2716 | (uri (bioconductor-uri "VariantTools" version)) |
| 2717 | (sha256 |
| 2718 | (base32 |
| 2719 | "0y37nziipwikg47x4jhhsx0dyv15rrih4a4z43jbzv4jgq4krzql")))) |
| 2720 | (properties `((upstream-name . "VariantTools"))) |
| 2721 | (build-system r-build-system) |
| 2722 | (propagated-inputs |
| 2723 | `(("r-biobase" ,r-biobase) |
| 2724 | ("r-biocgenerics" ,r-biocgenerics) |
| 2725 | ("r-biocparallel" ,r-biocparallel) |
| 2726 | ("r-biostrings" ,r-biostrings) |
| 2727 | ("r-bsgenome" ,r-bsgenome) |
| 2728 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 2729 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 2730 | ("r-genomicranges" ,r-genomicranges) |
| 2731 | ("r-iranges" ,r-iranges) |
| 2732 | ("r-matrix" ,r-matrix) |
| 2733 | ("r-rsamtools" ,r-rsamtools) |
| 2734 | ("r-rtracklayer" ,r-rtracklayer) |
| 2735 | ("r-s4vectors" ,r-s4vectors) |
| 2736 | ("r-variantannotation" ,r-variantannotation))) |
| 2737 | (home-page "https://bioconductor.org/packages/VariantTools/") |
| 2738 | (synopsis "Tools for exploratory analysis of variant calls") |
| 2739 | (description |
| 2740 | "Explore, diagnose, and compare variant calls using filters. The |
| 2741 | VariantTools package supports a workflow for loading data, calling single |
| 2742 | sample variants and tumor-specific somatic mutations or other sample-specific |
| 2743 | variant types (e.g., RNA editing). Most of the functions operate on |
| 2744 | alignments (BAM files) or datasets of called variants. The user is expected |
| 2745 | to have already aligned the reads with a separate tool, e.g., GSNAP via |
| 2746 | gmapR.") |
| 2747 | (license license:artistic2.0))) |
| 2748 | |
| 2749 | (define-public r-heatplus |
| 2750 | (package |
| 2751 | (name "r-heatplus") |
| 2752 | (version "2.30.0") |
| 2753 | (source |
| 2754 | (origin |
| 2755 | (method url-fetch) |
| 2756 | (uri (bioconductor-uri "Heatplus" version)) |
| 2757 | (sha256 |
| 2758 | (base32 |
| 2759 | "18b0zy12przp88sj1smvfdd39m17nhhnqzk656bs5pjls2ifmcm6")))) |
| 2760 | (properties `((upstream-name . "Heatplus"))) |
| 2761 | (build-system r-build-system) |
| 2762 | (propagated-inputs |
| 2763 | `(("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 2764 | (home-page "https://github.com/alexploner/Heatplus") |
| 2765 | (synopsis "Heatmaps with row and/or column covariates and colored clusters") |
| 2766 | (description |
| 2767 | "This package provides tools to display a rectangular heatmap (intensity |
| 2768 | plot) of a data matrix. By default, both samples (columns) and features (row) |
| 2769 | of the matrix are sorted according to a hierarchical clustering, and the |
| 2770 | corresponding dendrogram is plotted. Optionally, panels with additional |
| 2771 | information about samples and features can be added to the plot.") |
| 2772 | (license license:gpl2+))) |
| 2773 | |
| 2774 | (define-public r-gosemsim |
| 2775 | (package |
| 2776 | (name "r-gosemsim") |
| 2777 | (version "2.10.0") |
| 2778 | (source |
| 2779 | (origin |
| 2780 | (method url-fetch) |
| 2781 | (uri (bioconductor-uri "GOSemSim" version)) |
| 2782 | (sha256 |
| 2783 | (base32 |
| 2784 | "035jbm14rb1rjp2n00dp5bm88ad8a9afv4lvzpkv39nil98nzbdg")))) |
| 2785 | (properties `((upstream-name . "GOSemSim"))) |
| 2786 | (build-system r-build-system) |
| 2787 | (propagated-inputs |
| 2788 | `(("r-annotationdbi" ,r-annotationdbi) |
| 2789 | ("r-go-db" ,r-go-db) |
| 2790 | ("r-rcpp" ,r-rcpp))) |
| 2791 | (home-page "https://guangchuangyu.github.io/software/GOSemSim") |
| 2792 | (synopsis "GO-terms semantic similarity measures") |
| 2793 | (description |
| 2794 | "The semantic comparisons of @dfn{Gene Ontology} (GO) annotations provide |
| 2795 | quantitative ways to compute similarities between genes and gene groups, and |
| 2796 | have became important basis for many bioinformatics analysis approaches. |
| 2797 | GOSemSim is an R package for semantic similarity computation among GO terms, |
| 2798 | sets of GO terms, gene products and gene clusters.") |
| 2799 | (license license:artistic2.0))) |
| 2800 | |
| 2801 | (define-public r-anota |
| 2802 | (package |
| 2803 | (name "r-anota") |
| 2804 | (version "1.32.0") |
| 2805 | (source |
| 2806 | (origin |
| 2807 | (method url-fetch) |
| 2808 | (uri (bioconductor-uri "anota" version)) |
| 2809 | (sha256 |
| 2810 | (base32 |
| 2811 | "0jchhyf9gqyj0k0fn5zp319griy32cckqpldq9x58z69l2ix2s2c")))) |
| 2812 | (build-system r-build-system) |
| 2813 | (propagated-inputs |
| 2814 | `(("r-multtest" ,r-multtest) |
| 2815 | ("r-qvalue" ,r-qvalue))) |
| 2816 | (home-page "https://bioconductor.org/packages/anota/") |
| 2817 | (synopsis "Analysis of translational activity") |
| 2818 | (description |
| 2819 | "Genome wide studies of translational control is emerging as a tool to |
| 2820 | study verious biological conditions. The output from such analysis is both |
| 2821 | the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively |
| 2822 | involved in translation (the actively translating mRNA level) for each mRNA. |
| 2823 | The standard analysis of such data strives towards identifying differential |
| 2824 | translational between two or more sample classes - i.e. differences in |
| 2825 | actively translated mRNA levels that are independent of underlying differences |
| 2826 | in cytosolic mRNA levels. This package allows for such analysis using partial |
| 2827 | variances and the random variance model. As 10s of thousands of mRNAs are |
| 2828 | analyzed in parallell the library performs a number of tests to assure that |
| 2829 | the data set is suitable for such analysis.") |
| 2830 | (license license:gpl3))) |
| 2831 | |
| 2832 | (define-public r-sigpathway |
| 2833 | (package |
| 2834 | (name "r-sigpathway") |
| 2835 | (version "1.52.0") |
| 2836 | (source |
| 2837 | (origin |
| 2838 | (method url-fetch) |
| 2839 | (uri (bioconductor-uri "sigPathway" version)) |
| 2840 | (sha256 |
| 2841 | (base32 |
| 2842 | "1mc4lb78rcmpihzjiy4w738cbalw5zxms30z8kyy12s6vbxi6hx7")))) |
| 2843 | (properties `((upstream-name . "sigPathway"))) |
| 2844 | (build-system r-build-system) |
| 2845 | (home-page "https://www.pnas.org/cgi/doi/10.1073/pnas.0506577102") |
| 2846 | (synopsis "Pathway analysis") |
| 2847 | (description |
| 2848 | "This package is used to conduct pathway analysis by calculating the NT_k |
| 2849 | and NE_k statistics in a statistical framework for determining whether a |
| 2850 | specified group of genes for a pathway has a coordinated association with a |
| 2851 | phenotype of interest.") |
| 2852 | (license license:gpl2))) |
| 2853 | |
| 2854 | (define-public r-fgsea |
| 2855 | (package |
| 2856 | (name "r-fgsea") |
| 2857 | (version "1.10.0") |
| 2858 | (source |
| 2859 | (origin |
| 2860 | (method url-fetch) |
| 2861 | (uri (bioconductor-uri "fgsea" version)) |
| 2862 | (sha256 |
| 2863 | (base32 |
| 2864 | "07mvv1i690q80fm8sxgdqxchamn76409vn91ppgcck2xpi6b8q6c")))) |
| 2865 | (build-system r-build-system) |
| 2866 | (propagated-inputs |
| 2867 | `(("r-bh" ,r-bh) |
| 2868 | ("r-biocparallel" ,r-biocparallel) |
| 2869 | ("r-data-table" ,r-data-table) |
| 2870 | ("r-fastmatch" ,r-fastmatch) |
| 2871 | ("r-ggplot2" ,r-ggplot2) |
| 2872 | ("r-gridextra" ,r-gridextra) |
| 2873 | ("r-matrix" ,r-matrix) |
| 2874 | ("r-rcpp" ,r-rcpp))) |
| 2875 | (home-page "https://github.com/ctlab/fgsea/") |
| 2876 | (synopsis "Fast gene set enrichment analysis") |
| 2877 | (description |
| 2878 | "The package implements an algorithm for fast gene set enrichment |
| 2879 | analysis. Using the fast algorithm allows to make more permutations and get |
| 2880 | more fine grained p-values, which allows to use accurate stantard approaches |
| 2881 | to multiple hypothesis correction.") |
| 2882 | (license license:expat))) |
| 2883 | |
| 2884 | (define-public r-dose |
| 2885 | (package |
| 2886 | (name "r-dose") |
| 2887 | (version "3.10.0") |
| 2888 | (source |
| 2889 | (origin |
| 2890 | (method url-fetch) |
| 2891 | (uri (bioconductor-uri "DOSE" version)) |
| 2892 | (sha256 |
| 2893 | (base32 |
| 2894 | "0dvhnfhzhhzcxm8zhdwrkif7sak4p888sjqfd3a0p77h0hs6g8pv")))) |
| 2895 | (properties `((upstream-name . "DOSE"))) |
| 2896 | (build-system r-build-system) |
| 2897 | (propagated-inputs |
| 2898 | `(("r-annotationdbi" ,r-annotationdbi) |
| 2899 | ("r-biocparallel" ,r-biocparallel) |
| 2900 | ("r-do-db" ,r-do-db) |
| 2901 | ("r-fgsea" ,r-fgsea) |
| 2902 | ("r-ggplot2" ,r-ggplot2) |
| 2903 | ("r-gosemsim" ,r-gosemsim) |
| 2904 | ("r-qvalue" ,r-qvalue) |
| 2905 | ("r-reshape2" ,r-reshape2) |
| 2906 | ("r-s4vectors" ,r-s4vectors))) |
| 2907 | (home-page "https://guangchuangyu.github.io/software/DOSE/") |
| 2908 | (synopsis "Disease ontology semantic and enrichment analysis") |
| 2909 | (description |
| 2910 | "This package implements five methods proposed by Resnik, Schlicker, |
| 2911 | Jiang, Lin and Wang, respectively, for measuring semantic similarities among |
| 2912 | @dfn{Disease ontology} (DO) terms and gene products. Enrichment analyses |
| 2913 | including hypergeometric model and gene set enrichment analysis are also |
| 2914 | implemented for discovering disease associations of high-throughput biological |
| 2915 | data.") |
| 2916 | (license license:artistic2.0))) |
| 2917 | |
| 2918 | (define-public r-enrichplot |
| 2919 | (package |
| 2920 | (name "r-enrichplot") |
| 2921 | (version "1.4.0") |
| 2922 | (source |
| 2923 | (origin |
| 2924 | (method url-fetch) |
| 2925 | (uri (bioconductor-uri "enrichplot" version)) |
| 2926 | (sha256 |
| 2927 | (base32 |
| 2928 | "1i9psakvvdc6jn7k7zwpbdhwvf9r8s7649w05mwh1hy978x4rh6h")))) |
| 2929 | (build-system r-build-system) |
| 2930 | (propagated-inputs |
| 2931 | `(("r-annotationdbi" ,r-annotationdbi) |
| 2932 | ("r-cowplot" ,r-cowplot) |
| 2933 | ("r-dose" ,r-dose) |
| 2934 | ("r-europepmc" ,r-europepmc) |
| 2935 | ("r-ggplot2" ,r-ggplot2) |
| 2936 | ("r-ggplotify" ,r-ggplotify) |
| 2937 | ("r-ggraph" ,r-ggraph) |
| 2938 | ("r-ggridges" ,r-ggridges) |
| 2939 | ("r-gosemsim" ,r-gosemsim) |
| 2940 | ("r-gridextra" ,r-gridextra) |
| 2941 | ("r-igraph" ,r-igraph) |
| 2942 | ("r-purrr" ,r-purrr) |
| 2943 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 2944 | ("r-reshape2" ,r-reshape2) |
| 2945 | ("r-upsetr" ,r-upsetr))) |
| 2946 | (home-page "https://github.com/GuangchuangYu/enrichplot") |
| 2947 | (synopsis "Visualization of functional enrichment result") |
| 2948 | (description |
| 2949 | "The enrichplot package implements several visualization methods for |
| 2950 | interpreting functional enrichment results obtained from ORA or GSEA analyses. |
| 2951 | All the visualization methods are developed based on ggplot2 graphics.") |
| 2952 | (license license:artistic2.0))) |
| 2953 | |
| 2954 | (define-public r-clusterprofiler |
| 2955 | (package |
| 2956 | (name "r-clusterprofiler") |
| 2957 | (version "3.12.0") |
| 2958 | (source |
| 2959 | (origin |
| 2960 | (method url-fetch) |
| 2961 | (uri (bioconductor-uri "clusterProfiler" version)) |
| 2962 | (sha256 |
| 2963 | (base32 |
| 2964 | "1jw8h6nlcgd86qhqlcgi3icylb7amcqimlvzg29gay3bf3grwfhq")))) |
| 2965 | (properties |
| 2966 | `((upstream-name . "clusterProfiler"))) |
| 2967 | (build-system r-build-system) |
| 2968 | (propagated-inputs |
| 2969 | `(("r-annotationdbi" ,r-annotationdbi) |
| 2970 | ("r-dose" ,r-dose) |
| 2971 | ("r-enrichplot" ,r-enrichplot) |
| 2972 | ("r-ggplot2" ,r-ggplot2) |
| 2973 | ("r-go-db" ,r-go-db) |
| 2974 | ("r-gosemsim" ,r-gosemsim) |
| 2975 | ("r-magrittr" ,r-magrittr) |
| 2976 | ("r-plyr" ,r-plyr) |
| 2977 | ("r-qvalue" ,r-qvalue) |
| 2978 | ("r-rvcheck" ,r-rvcheck) |
| 2979 | ("r-tidyr" ,r-tidyr))) |
| 2980 | (home-page "https://guangchuangyu.github.io/software/clusterProfiler/") |
| 2981 | (synopsis "Analysis and visualization of functional profiles for gene clusters") |
| 2982 | (description |
| 2983 | "This package implements methods to analyze and visualize functional |
| 2984 | profiles (GO and KEGG) of gene and gene clusters.") |
| 2985 | (license license:artistic2.0))) |
| 2986 | |
| 2987 | (define-public r-mlinterfaces |
| 2988 | (package |
| 2989 | (name "r-mlinterfaces") |
| 2990 | (version "1.64.0") |
| 2991 | (source |
| 2992 | (origin |
| 2993 | (method url-fetch) |
| 2994 | (uri (bioconductor-uri "MLInterfaces" version)) |
| 2995 | (sha256 |
| 2996 | (base32 |
| 2997 | "0zqvxmvbkig3cc4r5k405s53d7y5ccvrf8kf5j6v8s1kkrklai4j")))) |
| 2998 | (properties `((upstream-name . "MLInterfaces"))) |
| 2999 | (build-system r-build-system) |
| 3000 | (propagated-inputs |
| 3001 | `(("r-annotate" ,r-annotate) |
| 3002 | ("r-biobase" ,r-biobase) |
| 3003 | ("r-biocgenerics" ,r-biocgenerics) |
| 3004 | ("r-cluster" ,r-cluster) |
| 3005 | ("r-fpc" ,r-fpc) |
| 3006 | ("r-gbm" ,r-gbm) |
| 3007 | ("r-gdata" ,r-gdata) |
| 3008 | ("r-genefilter" ,r-genefilter) |
| 3009 | ("r-ggvis" ,r-ggvis) |
| 3010 | ("r-hwriter" ,r-hwriter) |
| 3011 | ("r-mass" ,r-mass) |
| 3012 | ("r-mlbench" ,r-mlbench) |
| 3013 | ("r-pls" ,r-pls) |
| 3014 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 3015 | ("r-rda" ,r-rda) |
| 3016 | ("r-rpart" ,r-rpart) |
| 3017 | ("r-sfsmisc" ,r-sfsmisc) |
| 3018 | ("r-shiny" ,r-shiny) |
| 3019 | ("r-threejs" ,r-threejs))) |
| 3020 | (home-page "https://bioconductor.org/packages/MLInterfaces/") |
| 3021 | (synopsis "Interfaces to R machine learning procedures") |
| 3022 | (description |
| 3023 | "This package provides uniform interfaces to machine learning code for |
| 3024 | data in R and Bioconductor containers.") |
| 3025 | ;; Any version of the LGPL. |
| 3026 | (license license:lgpl2.1+))) |
| 3027 | |
| 3028 | (define-public r-annaffy |
| 3029 | (package |
| 3030 | (name "r-annaffy") |
| 3031 | (version "1.56.0") |
| 3032 | (source |
| 3033 | (origin |
| 3034 | (method url-fetch) |
| 3035 | (uri (bioconductor-uri "annaffy" version)) |
| 3036 | (sha256 |
| 3037 | (base32 |
| 3038 | "0sz96lcw0xc4bw1h3x0j40yh5ragmybsq6zwd0adlwzkhvriqjn9")))) |
| 3039 | (build-system r-build-system) |
| 3040 | (arguments |
| 3041 | `(#:phases |
| 3042 | (modify-phases %standard-phases |
| 3043 | (add-after 'unpack 'remove-reference-to-non-free-data |
| 3044 | (lambda _ |
| 3045 | (substitute* "DESCRIPTION" |
| 3046 | ((", KEGG.db") "")) |
| 3047 | #t))))) |
| 3048 | (propagated-inputs |
| 3049 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3050 | ("r-biobase" ,r-biobase) |
| 3051 | ("r-dbi" ,r-dbi) |
| 3052 | ("r-go-db" ,r-go-db))) |
| 3053 | (home-page "https://bioconductor.org/packages/annaffy/") |
| 3054 | (synopsis "Annotation tools for Affymetrix biological metadata") |
| 3055 | (description |
| 3056 | "This package provides functions for handling data from Bioconductor |
| 3057 | Affymetrix annotation data packages. It produces compact HTML and text |
| 3058 | reports including experimental data and URL links to many online databases. |
| 3059 | It allows searching of biological metadata using various criteria.") |
| 3060 | ;; Any version of the LGPL according to the DESCRIPTION file. A copy of |
| 3061 | ;; the LGPL 2.1 is included. |
| 3062 | (license license:lgpl2.1+))) |
| 3063 | |
| 3064 | (define-public r-a4core |
| 3065 | (package |
| 3066 | (name "r-a4core") |
| 3067 | (version "1.32.0") |
| 3068 | (source |
| 3069 | (origin |
| 3070 | (method url-fetch) |
| 3071 | (uri (bioconductor-uri "a4Core" version)) |
| 3072 | (sha256 |
| 3073 | (base32 |
| 3074 | "1cr0d1w81iygil3pygqzigfb1a0hc248qd9vqvs0n537cxrxq7i7")))) |
| 3075 | (properties `((upstream-name . "a4Core"))) |
| 3076 | (build-system r-build-system) |
| 3077 | (propagated-inputs |
| 3078 | `(("r-biobase" ,r-biobase) |
| 3079 | ("r-glmnet" ,r-glmnet))) |
| 3080 | (home-page "https://bioconductor.org/packages/a4Core") |
| 3081 | (synopsis "Automated Affymetrix array analysis core package") |
| 3082 | (description |
| 3083 | "This is the core package for the automated analysis of Affymetrix |
| 3084 | arrays.") |
| 3085 | (license license:gpl3))) |
| 3086 | |
| 3087 | (define-public r-a4classif |
| 3088 | (package |
| 3089 | (name "r-a4classif") |
| 3090 | (version "1.32.0") |
| 3091 | (source |
| 3092 | (origin |
| 3093 | (method url-fetch) |
| 3094 | (uri (bioconductor-uri "a4Classif" version)) |
| 3095 | (sha256 |
| 3096 | (base32 |
| 3097 | "1jif0w3hx020zzwkaza1a26mf34343y7a3v80ic93in6n53yjhj0")))) |
| 3098 | (properties `((upstream-name . "a4Classif"))) |
| 3099 | (build-system r-build-system) |
| 3100 | (propagated-inputs |
| 3101 | `(("r-a4core" ,r-a4core) |
| 3102 | ("r-a4preproc" ,r-a4preproc) |
| 3103 | ("r-glmnet" ,r-glmnet) |
| 3104 | ("r-mlinterfaces" ,r-mlinterfaces) |
| 3105 | ("r-pamr" ,r-pamr) |
| 3106 | ("r-rocr" ,r-rocr) |
| 3107 | ("r-varselrf" ,r-varselrf))) |
| 3108 | (home-page "https://bioconductor.org/packages/a4Classif/") |
| 3109 | (synopsis "Automated Affymetrix array analysis classification package") |
| 3110 | (description |
| 3111 | "This is the classification package for the automated analysis of |
| 3112 | Affymetrix arrays.") |
| 3113 | (license license:gpl3))) |
| 3114 | |
| 3115 | (define-public r-a4preproc |
| 3116 | (package |
| 3117 | (name "r-a4preproc") |
| 3118 | (version "1.32.0") |
| 3119 | (source |
| 3120 | (origin |
| 3121 | (method url-fetch) |
| 3122 | (uri (bioconductor-uri "a4Preproc" version)) |
| 3123 | (sha256 |
| 3124 | (base32 |
| 3125 | "13sj4zriq1mian2xcjwkbmmpdjh3h6dgjslar2hc8nmd34cb9xjr")))) |
| 3126 | (properties `((upstream-name . "a4Preproc"))) |
| 3127 | (build-system r-build-system) |
| 3128 | (propagated-inputs |
| 3129 | `(("r-annotationdbi" ,r-annotationdbi))) |
| 3130 | (home-page "https://bioconductor.org/packages/a4Preproc/") |
| 3131 | (synopsis "Automated Affymetrix array analysis preprocessing package") |
| 3132 | (description |
| 3133 | "This is a package for the automated analysis of Affymetrix arrays. It |
| 3134 | is used for preprocessing the arrays.") |
| 3135 | (license license:gpl3))) |
| 3136 | |
| 3137 | (define-public r-a4reporting |
| 3138 | (package |
| 3139 | (name "r-a4reporting") |
| 3140 | (version "1.32.0") |
| 3141 | (source |
| 3142 | (origin |
| 3143 | (method url-fetch) |
| 3144 | (uri (bioconductor-uri "a4Reporting" version)) |
| 3145 | (sha256 |
| 3146 | (base32 |
| 3147 | "1lail2iw8jmvfdq9brv7i41k6vmbhx2kp21jxq2cj1zva5rcqssj")))) |
| 3148 | (properties `((upstream-name . "a4Reporting"))) |
| 3149 | (build-system r-build-system) |
| 3150 | (propagated-inputs |
| 3151 | `(("r-annaffy" ,r-annaffy) |
| 3152 | ("r-xtable" ,r-xtable))) |
| 3153 | (home-page "https://bioconductor.org/packages/a4Reporting/") |
| 3154 | (synopsis "Automated Affymetrix array analysis reporting package") |
| 3155 | (description |
| 3156 | "This is a package for the automated analysis of Affymetrix arrays. It |
| 3157 | provides reporting features.") |
| 3158 | (license license:gpl3))) |
| 3159 | |
| 3160 | (define-public r-a4base |
| 3161 | (package |
| 3162 | (name "r-a4base") |
| 3163 | (version "1.32.0") |
| 3164 | (source |
| 3165 | (origin |
| 3166 | (method url-fetch) |
| 3167 | (uri (bioconductor-uri "a4Base" version)) |
| 3168 | (sha256 |
| 3169 | (base32 |
| 3170 | "0yd8gkg3dlkijnms88bxkqsghhc9i32pgd9yaq6hzr67wk879wa1")))) |
| 3171 | (properties `((upstream-name . "a4Base"))) |
| 3172 | (build-system r-build-system) |
| 3173 | (propagated-inputs |
| 3174 | `(("r-a4core" ,r-a4core) |
| 3175 | ("r-a4preproc" ,r-a4preproc) |
| 3176 | ("r-annaffy" ,r-annaffy) |
| 3177 | ("r-annotationdbi" ,r-annotationdbi) |
| 3178 | ("r-biobase" ,r-biobase) |
| 3179 | ("r-genefilter" ,r-genefilter) |
| 3180 | ("r-glmnet" ,r-glmnet) |
| 3181 | ("r-gplots" ,r-gplots) |
| 3182 | ("r-limma" ,r-limma) |
| 3183 | ("r-mpm" ,r-mpm) |
| 3184 | ("r-multtest" ,r-multtest))) |
| 3185 | (home-page "https://bioconductor.org/packages/a4Base/") |
| 3186 | (synopsis "Automated Affymetrix array analysis base package") |
| 3187 | (description |
| 3188 | "This package provides basic features for the automated analysis of |
| 3189 | Affymetrix arrays.") |
| 3190 | (license license:gpl3))) |
| 3191 | |
| 3192 | (define-public r-a4 |
| 3193 | (package |
| 3194 | (name "r-a4") |
| 3195 | (version "1.32.0") |
| 3196 | (source |
| 3197 | (origin |
| 3198 | (method url-fetch) |
| 3199 | (uri (bioconductor-uri "a4" version)) |
| 3200 | (sha256 |
| 3201 | (base32 |
| 3202 | "08146qzsr6mjblmh08g83063nnyrfl35z6p65v71isprkydgxyhy")))) |
| 3203 | (build-system r-build-system) |
| 3204 | (propagated-inputs |
| 3205 | `(("r-a4base" ,r-a4base) |
| 3206 | ("r-a4classif" ,r-a4classif) |
| 3207 | ("r-a4core" ,r-a4core) |
| 3208 | ("r-a4preproc" ,r-a4preproc) |
| 3209 | ("r-a4reporting" ,r-a4reporting))) |
| 3210 | (home-page "https://bioconductor.org/packages/a4/") |
| 3211 | (synopsis "Automated Affymetrix array analysis umbrella package") |
| 3212 | (description |
| 3213 | "This package provides a software suite for the automated analysis of |
| 3214 | Affymetrix arrays.") |
| 3215 | (license license:gpl3))) |
| 3216 | |
| 3217 | (define-public r-abseqr |
| 3218 | (package |
| 3219 | (name "r-abseqr") |
| 3220 | (version "1.2.0") |
| 3221 | (source |
| 3222 | (origin |
| 3223 | (method url-fetch) |
| 3224 | (uri (bioconductor-uri "abseqR" version)) |
| 3225 | (sha256 |
| 3226 | (base32 |
| 3227 | "0cbjm7cxjfrkwqhcrrh93w0zf3skmi2p9hyx7acg0ym5fz0ic51r")))) |
| 3228 | (properties `((upstream-name . "abseqR"))) |
| 3229 | (build-system r-build-system) |
| 3230 | (inputs |
| 3231 | `(("pandoc" ,ghc-pandoc))) |
| 3232 | (propagated-inputs |
| 3233 | `(("r-biocparallel" ,r-biocparallel) |
| 3234 | ("r-biocstyle" ,r-biocstyle) |
| 3235 | ("r-circlize" ,r-circlize) |
| 3236 | ("r-flexdashboard" ,r-flexdashboard) |
| 3237 | ("r-ggcorrplot" ,r-ggcorrplot) |
| 3238 | ("r-ggdendro" ,r-ggdendro) |
| 3239 | ("r-ggplot2" ,r-ggplot2) |
| 3240 | ("r-gridextra" ,r-gridextra) |
| 3241 | ("r-knitr" ,r-knitr) |
| 3242 | ("r-plotly" ,r-plotly) |
| 3243 | ("r-plyr" ,r-plyr) |
| 3244 | ("r-png" ,r-png) |
| 3245 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 3246 | ("r-reshape2" ,r-reshape2) |
| 3247 | ("r-rmarkdown" ,r-rmarkdown) |
| 3248 | ("r-stringr" ,r-stringr) |
| 3249 | ("r-vegan" ,r-vegan) |
| 3250 | ("r-venndiagram" ,r-venndiagram))) |
| 3251 | (home-page "https://github.com/malhamdoosh/abseqR") |
| 3252 | (synopsis "Reporting and data analysis for Rep-Seq datasets of antibody libraries") |
| 3253 | (description |
| 3254 | "AbSeq is a comprehensive bioinformatic pipeline for the analysis of |
| 3255 | sequencing datasets generated from antibody libraries and abseqR is one of its |
| 3256 | packages. AbseqR empowers the users of abseqPy with plotting and reporting |
| 3257 | capabilities and allows them to generate interactive HTML reports for the |
| 3258 | convenience of viewing and sharing with other researchers. Additionally, |
| 3259 | abseqR extends abseqPy to compare multiple repertoire analyses and perform |
| 3260 | further downstream analysis on its output.") |
| 3261 | (license license:gpl3))) |
| 3262 | |
| 3263 | (define-public r-bacon |
| 3264 | (package |
| 3265 | (name "r-bacon") |
| 3266 | (version "1.12.0") |
| 3267 | (source |
| 3268 | (origin |
| 3269 | (method url-fetch) |
| 3270 | (uri (bioconductor-uri "bacon" version)) |
| 3271 | (sha256 |
| 3272 | (base32 |
| 3273 | "1p6h348kwbsan6dwviclwxx02jcdmf580g5f95w2sgn4jnfv7q1q")))) |
| 3274 | (build-system r-build-system) |
| 3275 | (propagated-inputs |
| 3276 | `(("r-biocparallel" ,r-biocparallel) |
| 3277 | ("r-ellipse" ,r-ellipse) |
| 3278 | ("r-ggplot2" ,r-ggplot2))) |
| 3279 | (home-page "https://bioconductor.org/packages/bacon/") |
| 3280 | (synopsis "Controlling bias and inflation in association studies") |
| 3281 | (description |
| 3282 | "Bacon can be used to remove inflation and bias often observed in |
| 3283 | epigenome- and transcriptome-wide association studies. To this end bacon |
| 3284 | constructs an empirical null distribution using a Gibbs Sampling algorithm by |
| 3285 | fitting a three-component normal mixture on z-scores.") |
| 3286 | (license license:gpl2+))) |
| 3287 | |
| 3288 | (define-public r-rgadem |
| 3289 | (package |
| 3290 | (name "r-rgadem") |
| 3291 | (version "2.31.0") |
| 3292 | (source |
| 3293 | (origin |
| 3294 | (method url-fetch) |
| 3295 | (uri (bioconductor-uri "rGADEM" version)) |
| 3296 | (sha256 |
| 3297 | (base32 |
| 3298 | "0mck3dsxzjxszfs1cl96kd83q7n85p3763s0y3gwws69jn7p6w5j")))) |
| 3299 | (properties `((upstream-name . "rGADEM"))) |
| 3300 | (build-system r-build-system) |
| 3301 | (propagated-inputs |
| 3302 | `(("r-biostrings" ,r-biostrings) |
| 3303 | ("r-bsgenome" ,r-bsgenome) |
| 3304 | ("r-iranges" ,r-iranges) |
| 3305 | ("r-seqlogo" ,r-seqlogo))) |
| 3306 | (home-page "https://bioconductor.org/packages/rGADEM/") |
| 3307 | (synopsis "De novo sequence motif discovery") |
| 3308 | (description |
| 3309 | "rGADEM is an efficient de novo motif discovery tool for large-scale |
| 3310 | genomic sequence data.") |
| 3311 | (license license:artistic2.0))) |
| 3312 | |
| 3313 | (define-public r-motiv |
| 3314 | (package |
| 3315 | (name "r-motiv") |
| 3316 | (version "1.40.0") |
| 3317 | (source |
| 3318 | (origin |
| 3319 | (method url-fetch) |
| 3320 | (uri (bioconductor-uri "MotIV" version)) |
| 3321 | (sha256 |
| 3322 | (base32 |
| 3323 | "088z3vyx5h2c4ll4sway01cd4h0x2ayhbv55f6l2kss71v6k6byf")))) |
| 3324 | (properties `((upstream-name . "MotIV"))) |
| 3325 | (build-system r-build-system) |
| 3326 | (inputs |
| 3327 | `(("gsl" ,gsl))) |
| 3328 | (propagated-inputs |
| 3329 | `(("r-biocgenerics" ,r-biocgenerics) |
| 3330 | ("r-biostrings" ,r-biostrings) |
| 3331 | ("r-iranges" ,r-iranges) |
| 3332 | ("r-lattice" ,r-lattice) |
| 3333 | ("r-rgadem" ,r-rgadem) |
| 3334 | ("r-s4vectors" ,r-s4vectors))) |
| 3335 | (home-page "https://bioconductor.org/packages/MotIV/") |
| 3336 | (synopsis "Motif identification and validation") |
| 3337 | (description |
| 3338 | "This package is used for the identification and validation of sequence |
| 3339 | motifs. It makes use of STAMP for comparing a set of motifs to a given |
| 3340 | database (e.g. JASPAR). It can also be used to visualize motifs, motif |
| 3341 | distributions, modules and filter motifs.") |
| 3342 | (license license:gpl2))) |
| 3343 | |
| 3344 | (define-public r-motifstack |
| 3345 | (package |
| 3346 | (name "r-motifstack") |
| 3347 | (version "1.26.0") |
| 3348 | (source |
| 3349 | (origin |
| 3350 | (method url-fetch) |
| 3351 | (uri (bioconductor-uri "motifStack" version)) |
| 3352 | (sha256 |
| 3353 | (base32 |
| 3354 | "1c4w39ilc4ca4wgi1b6iypadkbxvqjw7k2br0d7q03niw9qjkhxf")))) |
| 3355 | (properties `((upstream-name . "motifStack"))) |
| 3356 | (build-system r-build-system) |
| 3357 | (propagated-inputs |
| 3358 | `(("r-ade4" ,r-ade4) |
| 3359 | ("r-biostrings" ,r-biostrings) |
| 3360 | ("r-grimport" ,r-grimport) |
| 3361 | ("r-htmlwidgets" ,r-htmlwidgets) |
| 3362 | ("r-motiv" ,r-motiv) |
| 3363 | ("r-scales" ,r-scales) |
| 3364 | ("r-xml" ,r-xml))) |
| 3365 | (home-page "https://bioconductor.org/packages/motifStack/") |
| 3366 | (synopsis "Plot stacked logos for DNA, RNA and amino acid sequences") |
| 3367 | (description |
| 3368 | "The motifStack package is designed for graphic representation of |
| 3369 | multiple motifs with different similarity scores. It works with both DNA/RNA |
| 3370 | sequence motifs and amino acid sequence motifs. In addition, it provides the |
| 3371 | flexibility for users to customize the graphic parameters such as the font |
| 3372 | type and symbol colors.") |
| 3373 | (license license:gpl2+))) |
| 3374 | |
| 3375 | (define-public r-genomicscores |
| 3376 | (package |
| 3377 | (name "r-genomicscores") |
| 3378 | (version "1.6.0") |
| 3379 | (source |
| 3380 | (origin |
| 3381 | (method url-fetch) |
| 3382 | (uri (bioconductor-uri "GenomicScores" version)) |
| 3383 | (sha256 |
| 3384 | (base32 |
| 3385 | "0lrhkcblvnki6kncwpavs01gbcz22yza6ma8zvfmbrrkfaxqzh8n")))) |
| 3386 | (properties `((upstream-name . "GenomicScores"))) |
| 3387 | (build-system r-build-system) |
| 3388 | (propagated-inputs |
| 3389 | `(("r-annotationhub" ,r-annotationhub) |
| 3390 | ("r-biobase" ,r-biobase) |
| 3391 | ("r-biocgenerics" ,r-biocgenerics) |
| 3392 | ("r-biostrings" ,r-biostrings) |
| 3393 | ("r-bsgenome" ,r-bsgenome) |
| 3394 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3395 | ("r-genomicranges" ,r-genomicranges) |
| 3396 | ("r-iranges" ,r-iranges) |
| 3397 | ("r-s4vectors" ,r-s4vectors) |
| 3398 | ("r-xml" ,r-xml))) |
| 3399 | (home-page "https://github.com/rcastelo/GenomicScores/") |
| 3400 | (synopsis "Work with genome-wide position-specific scores") |
| 3401 | (description |
| 3402 | "This package provides infrastructure to store and access genome-wide |
| 3403 | position-specific scores within R and Bioconductor.") |
| 3404 | (license license:artistic2.0))) |
| 3405 | |
| 3406 | (define-public r-atacseqqc |
| 3407 | (package |
| 3408 | (name "r-atacseqqc") |
| 3409 | (version "1.6.4") |
| 3410 | (source |
| 3411 | (origin |
| 3412 | (method url-fetch) |
| 3413 | (uri (bioconductor-uri "ATACseqQC" version)) |
| 3414 | (sha256 |
| 3415 | (base32 |
| 3416 | "1rblvqar11fib6ip2hq0756vqi6qmncf90jw6i5p5lrgzmaxy8hn")))) |
| 3417 | (properties `((upstream-name . "ATACseqQC"))) |
| 3418 | (build-system r-build-system) |
| 3419 | (propagated-inputs |
| 3420 | `(("r-biocgenerics" ,r-biocgenerics) |
| 3421 | ("r-biostrings" ,r-biostrings) |
| 3422 | ("r-bsgenome" ,r-bsgenome) |
| 3423 | ("r-chippeakanno" ,r-chippeakanno) |
| 3424 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3425 | ("r-genomicalignments" ,r-genomicalignments) |
| 3426 | ("r-genomicranges" ,r-genomicranges) |
| 3427 | ("r-genomicscores" ,r-genomicscores) |
| 3428 | ("r-iranges" ,r-iranges) |
| 3429 | ("r-kernsmooth" ,r-kernsmooth) |
| 3430 | ("r-limma" ,r-limma) |
| 3431 | ("r-motifstack" ,r-motifstack) |
| 3432 | ("r-preseqr" ,r-preseqr) |
| 3433 | ("r-randomforest" ,r-randomforest) |
| 3434 | ("r-rsamtools" ,r-rsamtools) |
| 3435 | ("r-rtracklayer" ,r-rtracklayer) |
| 3436 | ("r-s4vectors" ,r-s4vectors))) |
| 3437 | (home-page "https://bioconductor.org/packages/ATACseqQC/") |
| 3438 | (synopsis "ATAC-seq quality control") |
| 3439 | (description |
| 3440 | "ATAC-seq, an assay for Transposase-Accessible Chromatin using |
| 3441 | sequencing, is a rapid and sensitive method for chromatin accessibility |
| 3442 | analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq |
| 3443 | and DNAse-seq. The ATACseqQC package was developed to help users to quickly |
| 3444 | assess whether their ATAC-seq experiment is successful. It includes |
| 3445 | diagnostic plots of fragment size distribution, proportion of mitochondria |
| 3446 | reads, nucleosome positioning pattern, and CTCF or other Transcript Factor |
| 3447 | footprints.") |
| 3448 | (license license:gpl2+))) |
| 3449 | |
| 3450 | (define-public r-gofuncr |
| 3451 | (package |
| 3452 | (name "r-gofuncr") |
| 3453 | (version "1.2.0") |
| 3454 | (source |
| 3455 | (origin |
| 3456 | (method url-fetch) |
| 3457 | (uri (bioconductor-uri "GOfuncR" version)) |
| 3458 | (sha256 |
| 3459 | (base32 |
| 3460 | "021kgcbm8n2yalhzab11cyppwznlkglynnh45wsgy9i2vi2n2znk")))) |
| 3461 | (properties `((upstream-name . "GOfuncR"))) |
| 3462 | (build-system r-build-system) |
| 3463 | (propagated-inputs |
| 3464 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3465 | ("r-genomicranges" ,r-genomicranges) |
| 3466 | ("r-gtools" ,r-gtools) |
| 3467 | ("r-iranges" ,r-iranges) |
| 3468 | ("r-mapplots" ,r-mapplots) |
| 3469 | ("r-rcpp" ,r-rcpp) |
| 3470 | ("r-vioplot" ,r-vioplot))) |
| 3471 | (home-page "https://bioconductor.org/packages/GOfuncR/") |
| 3472 | (synopsis "Gene ontology enrichment using FUNC") |
| 3473 | (description |
| 3474 | "GOfuncR performs a gene ontology enrichment analysis based on the |
| 3475 | ontology enrichment software FUNC. GO-annotations are obtained from |
| 3476 | OrganismDb or OrgDb packages (@code{Homo.sapiens} by default); the GO-graph is |
| 3477 | included in the package and updated regularly. GOfuncR provides the standard |
| 3478 | candidate vs background enrichment analysis using the hypergeometric test, as |
| 3479 | well as three additional tests: |
| 3480 | |
| 3481 | @enumerate |
| 3482 | @item the Wilcoxon rank-sum test that is used when genes are ranked, |
| 3483 | @item a binomial test that is used when genes are associated with two counts, |
| 3484 | and |
| 3485 | @item a Chi-square or Fisher's exact test that is used in cases when genes are |
| 3486 | associated with four counts. |
| 3487 | @end enumerate |
| 3488 | |
| 3489 | To correct for multiple testing and interdependency of the tests, family-wise |
| 3490 | error rates are computed based on random permutations of the gene-associated |
| 3491 | variables. GOfuncR also provides tools for exploring the ontology graph and |
| 3492 | the annotations, and options to take gene-length or spatial clustering of |
| 3493 | genes into account. It is also possible to provide custom gene coordinates, |
| 3494 | annotations and ontologies.") |
| 3495 | (license license:gpl2+))) |
| 3496 | |
| 3497 | (define-public r-abaenrichment |
| 3498 | (package |
| 3499 | (name "r-abaenrichment") |
| 3500 | (version "1.12.0") |
| 3501 | (source |
| 3502 | (origin |
| 3503 | (method url-fetch) |
| 3504 | (uri (bioconductor-uri "ABAEnrichment" version)) |
| 3505 | (sha256 |
| 3506 | (base32 |
| 3507 | "0bvanqmg1smyckh16m2qn7d68zq4j7n74sgsnbgms5jngbp9158v")))) |
| 3508 | (properties `((upstream-name . "ABAEnrichment"))) |
| 3509 | (build-system r-build-system) |
| 3510 | (propagated-inputs |
| 3511 | `(("r-abadata" ,r-abadata) |
| 3512 | ("r-data-table" ,r-data-table) |
| 3513 | ("r-gofuncr" ,r-gofuncr) |
| 3514 | ("r-gplots" ,r-gplots) |
| 3515 | ("r-gtools" ,r-gtools) |
| 3516 | ("r-rcpp" ,r-rcpp))) |
| 3517 | (home-page "https://bioconductor.org/packages/ABAEnrichment/") |
| 3518 | (synopsis "Gene expression enrichment in human brain regions") |
| 3519 | (description |
| 3520 | "The package ABAEnrichment is designed to test for enrichment of user |
| 3521 | defined candidate genes in the set of expressed genes in different human brain |
| 3522 | regions. The core function @code{aba_enrich} integrates the expression of the |
| 3523 | candidate gene set (averaged across donors) and the structural information of |
| 3524 | the brain using an ontology, both provided by the Allen Brain Atlas project.") |
| 3525 | (license license:gpl2+))) |
| 3526 | |
| 3527 | (define-public r-annotationfuncs |
| 3528 | (package |
| 3529 | (name "r-annotationfuncs") |
| 3530 | (version "1.32.0") |
| 3531 | (source |
| 3532 | (origin |
| 3533 | (method url-fetch) |
| 3534 | (uri (bioconductor-uri "AnnotationFuncs" version)) |
| 3535 | (sha256 |
| 3536 | (base32 |
| 3537 | "1x11mfabh7kbp39y5rkmrpjkaawx7ab5anfmciamrmrcw1kddbss")))) |
| 3538 | (properties |
| 3539 | `((upstream-name . "AnnotationFuncs"))) |
| 3540 | (build-system r-build-system) |
| 3541 | (propagated-inputs |
| 3542 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3543 | ("r-dbi" ,r-dbi))) |
| 3544 | (home-page "https://www.iysik.com/r/annotationfuncs") |
| 3545 | (synopsis "Annotation translation functions") |
| 3546 | (description |
| 3547 | "This package provides functions for handling translating between |
| 3548 | different identifieres using the Biocore Data Team data-packages (e.g. |
| 3549 | @code{org.Bt.eg.db}).") |
| 3550 | (license license:gpl2))) |
| 3551 | |
| 3552 | (define-public r-annotationtools |
| 3553 | (package |
| 3554 | (name "r-annotationtools") |
| 3555 | (version "1.56.0") |
| 3556 | (source |
| 3557 | (origin |
| 3558 | (method url-fetch) |
| 3559 | (uri (bioconductor-uri "annotationTools" version)) |
| 3560 | (sha256 |
| 3561 | (base32 |
| 3562 | "0hqy0mq6pkn05p2dv4pw24p697yvikhdn351adf2ynldy6f3sl9z")))) |
| 3563 | (properties |
| 3564 | `((upstream-name . "annotationTools"))) |
| 3565 | (build-system r-build-system) |
| 3566 | (propagated-inputs `(("r-biobase" ,r-biobase))) |
| 3567 | (home-page "https://bioconductor.org/packages/annotationTools/") |
| 3568 | (synopsis "Annotate microarrays and perform gene expression analyses") |
| 3569 | (description |
| 3570 | "This package provides functions to annotate microarrays, find orthologs, |
| 3571 | and integrate heterogeneous gene expression profiles using annotation and |
| 3572 | other molecular biology information available as flat file database (plain |
| 3573 | text files).") |
| 3574 | ;; Any version of the GPL. |
| 3575 | (license (list license:gpl2+)))) |
| 3576 | |
| 3577 | (define-public r-allelicimbalance |
| 3578 | (package |
| 3579 | (name "r-allelicimbalance") |
| 3580 | (version "1.20.0") |
| 3581 | (source |
| 3582 | (origin |
| 3583 | (method url-fetch) |
| 3584 | (uri (bioconductor-uri "AllelicImbalance" version)) |
| 3585 | (sha256 |
| 3586 | (base32 |
| 3587 | "03524lj6aw9cskbpxzjmi9g708x6p94mf26yz4j941g1d0mc3z91")))) |
| 3588 | (properties |
| 3589 | `((upstream-name . "AllelicImbalance"))) |
| 3590 | (build-system r-build-system) |
| 3591 | (propagated-inputs |
| 3592 | `(("r-annotationdbi" ,r-annotationdbi) |
| 3593 | ("r-biocgenerics" ,r-biocgenerics) |
| 3594 | ("r-biostrings" ,r-biostrings) |
| 3595 | ("r-bsgenome" ,r-bsgenome) |
| 3596 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3597 | ("r-genomicalignments" ,r-genomicalignments) |
| 3598 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 3599 | ("r-genomicranges" ,r-genomicranges) |
| 3600 | ("r-gridextra" ,r-gridextra) |
| 3601 | ("r-gviz" ,r-gviz) |
| 3602 | ("r-iranges" ,r-iranges) |
| 3603 | ("r-lattice" ,r-lattice) |
| 3604 | ("r-latticeextra" ,r-latticeextra) |
| 3605 | ("r-nlme" ,r-nlme) |
| 3606 | ("r-rsamtools" ,r-rsamtools) |
| 3607 | ("r-s4vectors" ,r-s4vectors) |
| 3608 | ("r-seqinr" ,r-seqinr) |
| 3609 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 3610 | ("r-variantannotation" ,r-variantannotation))) |
| 3611 | (home-page "https://github.com/pappewaio/AllelicImbalance") |
| 3612 | (synopsis "Investigate allele-specific expression") |
| 3613 | (description |
| 3614 | "This package provides a framework for allele-specific expression |
| 3615 | investigation using RNA-seq data.") |
| 3616 | (license license:gpl3))) |
| 3617 | |
| 3618 | (define-public r-aucell |
| 3619 | (package |
| 3620 | (name "r-aucell") |
| 3621 | (version "1.4.1") |
| 3622 | (source |
| 3623 | (origin |
| 3624 | (method url-fetch) |
| 3625 | (uri (bioconductor-uri "AUCell" version)) |
| 3626 | (sha256 |
| 3627 | (base32 |
| 3628 | "1kdrs0521cyb8wlc4i3idfprrcy2f9w6kl56hfa94n0brmx62ya9")))) |
| 3629 | (properties `((upstream-name . "AUCell"))) |
| 3630 | (build-system r-build-system) |
| 3631 | (propagated-inputs |
| 3632 | `(("r-data-table" ,r-data-table) |
| 3633 | ("r-gseabase" ,r-gseabase) |
| 3634 | ("r-mixtools" ,r-mixtools) |
| 3635 | ("r-r-utils" ,r-r-utils) |
| 3636 | ("r-shiny" ,r-shiny) |
| 3637 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 3638 | (home-page "https://bioconductor.org/packages/AUCell/") |
| 3639 | (synopsis "Analysis of gene set activity in single-cell RNA-seq data") |
| 3640 | (description |
| 3641 | "AUCell allows to identify cells with active gene sets (e.g. signatures, |
| 3642 | gene modules, etc) in single-cell RNA-seq data. AUCell uses the @dfn{Area |
| 3643 | Under the Curve} (AUC) to calculate whether a critical subset of the input |
| 3644 | gene set is enriched within the expressed genes for each cell. The |
| 3645 | distribution of AUC scores across all the cells allows exploring the relative |
| 3646 | expression of the signature. Since the scoring method is ranking-based, |
| 3647 | AUCell is independent of the gene expression units and the normalization |
| 3648 | procedure. In addition, since the cells are evaluated individually, it can |
| 3649 | easily be applied to bigger datasets, subsetting the expression matrix if |
| 3650 | needed.") |
| 3651 | (license license:gpl3))) |
| 3652 | |
| 3653 | (define-public r-ebimage |
| 3654 | (package |
| 3655 | (name "r-ebimage") |
| 3656 | (version "4.24.0") |
| 3657 | (source |
| 3658 | (origin |
| 3659 | (method url-fetch) |
| 3660 | (uri (bioconductor-uri "EBImage" version)) |
| 3661 | (sha256 |
| 3662 | (base32 |
| 3663 | "18v2zr7xh0d0xbs7mxa2b6xjqlqiml0hji27gq1351xp5bf2pxvx")))) |
| 3664 | (properties `((upstream-name . "EBImage"))) |
| 3665 | (build-system r-build-system) |
| 3666 | (propagated-inputs |
| 3667 | `(("r-abind" ,r-abind) |
| 3668 | ("r-biocgenerics" ,r-biocgenerics) |
| 3669 | ("r-fftwtools" ,r-fftwtools) |
| 3670 | ("r-htmltools" ,r-htmltools) |
| 3671 | ("r-htmlwidgets" ,r-htmlwidgets) |
| 3672 | ("r-jpeg" ,r-jpeg) |
| 3673 | ("r-locfit" ,r-locfit) |
| 3674 | ("r-png" ,r-png) |
| 3675 | ("r-rcurl" ,r-rcurl) |
| 3676 | ("r-tiff" ,r-tiff))) |
| 3677 | (native-inputs |
| 3678 | `(("r-knitr" ,r-knitr))) ; for vignettes |
| 3679 | (home-page "https://github.com/aoles/EBImage") |
| 3680 | (synopsis "Image processing and analysis toolbox for R") |
| 3681 | (description |
| 3682 | "EBImage provides general purpose functionality for image processing and |
| 3683 | analysis. In the context of (high-throughput) microscopy-based cellular |
| 3684 | assays, EBImage offers tools to segment cells and extract quantitative |
| 3685 | cellular descriptors. This allows the automation of such tasks using the R |
| 3686 | programming language and facilitates the use of other tools in the R |
| 3687 | environment for signal processing, statistical modeling, machine learning and |
| 3688 | visualization with image data.") |
| 3689 | ;; Any version of the LGPL. |
| 3690 | (license license:lgpl2.1+))) |
| 3691 | |
| 3692 | (define-public r-yamss |
| 3693 | (package |
| 3694 | (name "r-yamss") |
| 3695 | (version "1.8.1") |
| 3696 | (source |
| 3697 | (origin |
| 3698 | (method url-fetch) |
| 3699 | (uri (bioconductor-uri "yamss" version)) |
| 3700 | (sha256 |
| 3701 | (base32 |
| 3702 | "13pln09j08fjsr7bj17apy4j0sr79n7jzshi8jbnz57jil7k6ia9")))) |
| 3703 | (build-system r-build-system) |
| 3704 | (propagated-inputs |
| 3705 | `(("r-biocgenerics" ,r-biocgenerics) |
| 3706 | ("r-data-table" ,r-data-table) |
| 3707 | ("r-ebimage" ,r-ebimage) |
| 3708 | ("r-iranges" ,r-iranges) |
| 3709 | ("r-limma" ,r-limma) |
| 3710 | ("r-matrix" ,r-matrix) |
| 3711 | ("r-mzr" ,r-mzr) |
| 3712 | ("r-s4vectors" ,r-s4vectors) |
| 3713 | ("r-summarizedexperiment" |
| 3714 | ,r-summarizedexperiment))) |
| 3715 | (home-page "https://github.com/hansenlab/yamss") |
| 3716 | (synopsis "Tools for high-throughput metabolomics") |
| 3717 | (description |
| 3718 | "This package provides tools to analyze and visualize high-throughput |
| 3719 | metabolomics data acquired using chromatography-mass spectrometry. These tools |
| 3720 | preprocess data in a way that enables reliable and powerful differential |
| 3721 | analysis.") |
| 3722 | (license license:artistic2.0))) |
| 3723 | |
| 3724 | (define-public r-gtrellis |
| 3725 | (package |
| 3726 | (name "r-gtrellis") |
| 3727 | (version "1.14.0") |
| 3728 | (source |
| 3729 | (origin |
| 3730 | (method url-fetch) |
| 3731 | (uri (bioconductor-uri "gtrellis" version)) |
| 3732 | (sha256 |
| 3733 | (base32 |
| 3734 | "17c43vs6m6hj90x5is0pbcpcv59gg9z98c47hnvlypgcqch38h6v")))) |
| 3735 | (build-system r-build-system) |
| 3736 | (propagated-inputs |
| 3737 | `(("r-circlize" ,r-circlize) |
| 3738 | ("r-genomicranges" ,r-genomicranges) |
| 3739 | ("r-getoptlong" ,r-getoptlong) |
| 3740 | ("r-iranges" ,r-iranges))) |
| 3741 | (home-page "https://github.com/jokergoo/gtrellis") |
| 3742 | (synopsis "Genome level Trellis layout") |
| 3743 | (description |
| 3744 | "Genome level Trellis graph visualizes genomic data conditioned by |
| 3745 | genomic categories (e.g. chromosomes). For each genomic category, multiple |
| 3746 | dimensional data which are represented as tracks describe different features |
| 3747 | from different aspects. This package provides high flexibility to arrange |
| 3748 | genomic categories and to add self-defined graphics in the plot.") |
| 3749 | (license license:expat))) |
| 3750 | |
| 3751 | (define-public r-somaticsignatures |
| 3752 | (package |
| 3753 | (name "r-somaticsignatures") |
| 3754 | (version "2.18.0") |
| 3755 | (source |
| 3756 | (origin |
| 3757 | (method url-fetch) |
| 3758 | (uri (bioconductor-uri "SomaticSignatures" version)) |
| 3759 | (sha256 |
| 3760 | (base32 |
| 3761 | "013dslbyq55a41d3n842brjk2bq1kxw0r18mb6drgbxx2sflzc02")))) |
| 3762 | (properties |
| 3763 | `((upstream-name . "SomaticSignatures"))) |
| 3764 | (build-system r-build-system) |
| 3765 | (propagated-inputs |
| 3766 | `(("r-biobase" ,r-biobase) |
| 3767 | ("r-biostrings" ,r-biostrings) |
| 3768 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3769 | ("r-genomicranges" ,r-genomicranges) |
| 3770 | ("r-ggbio" ,r-ggbio) |
| 3771 | ("r-ggplot2" ,r-ggplot2) |
| 3772 | ("r-iranges" ,r-iranges) |
| 3773 | ("r-nmf" ,r-nmf) |
| 3774 | ("r-pcamethods" ,r-pcamethods) |
| 3775 | ("r-proxy" ,r-proxy) |
| 3776 | ("r-reshape2" ,r-reshape2) |
| 3777 | ("r-s4vectors" ,r-s4vectors) |
| 3778 | ("r-variantannotation" ,r-variantannotation))) |
| 3779 | (home-page "https://github.com/juliangehring/SomaticSignatures") |
| 3780 | (synopsis "Somatic signatures") |
| 3781 | (description |
| 3782 | "This package identifies mutational signatures of @dfn{single nucleotide |
| 3783 | variants} (SNVs). It provides a infrastructure related to the methodology |
| 3784 | described in Nik-Zainal (2012, Cell), with flexibility in the matrix |
| 3785 | decomposition algorithms.") |
| 3786 | (license license:expat))) |
| 3787 | |
| 3788 | (define-public r-yapsa |
| 3789 | (package |
| 3790 | (name "r-yapsa") |
| 3791 | (version "1.8.0") |
| 3792 | (source |
| 3793 | (origin |
| 3794 | (method url-fetch) |
| 3795 | (uri (bioconductor-uri "YAPSA" version)) |
| 3796 | (sha256 |
| 3797 | (base32 |
| 3798 | "1agacimdd1m5yja2xbcsb83mns4svpxbjcsfrvm9ydqdj737i10j")))) |
| 3799 | (properties `((upstream-name . "YAPSA"))) |
| 3800 | (build-system r-build-system) |
| 3801 | (propagated-inputs |
| 3802 | `(("r-circlize" ,r-circlize) |
| 3803 | ("r-complexheatmap" ,r-complexheatmap) |
| 3804 | ("r-corrplot" ,r-corrplot) |
| 3805 | ("r-dendextend" ,r-dendextend) |
| 3806 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3807 | ("r-genomicranges" ,r-genomicranges) |
| 3808 | ("r-getoptlong" ,r-getoptlong) |
| 3809 | ("r-ggplot2" ,r-ggplot2) |
| 3810 | ("r-gridextra" ,r-gridextra) |
| 3811 | ("r-gtrellis" ,r-gtrellis) |
| 3812 | ("r-keggrest" ,r-keggrest) |
| 3813 | ("r-lsei" ,r-lsei) |
| 3814 | ("r-pmcmr" ,r-pmcmr) |
| 3815 | ("r-reshape2" ,r-reshape2) |
| 3816 | ("r-somaticsignatures" ,r-somaticsignatures) |
| 3817 | ("r-variantannotation" ,r-variantannotation))) |
| 3818 | (home-page "https://bioconductor.org/packages/YAPSA/") |
| 3819 | (synopsis "Yet another package for signature analysis") |
| 3820 | (description |
| 3821 | "This package provides functions and routines useful in the analysis of |
| 3822 | somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, |
| 3823 | functions to perform a signature analysis with known signatures and a |
| 3824 | signature analysis on @dfn{stratified mutational catalogue} (SMC) are |
| 3825 | provided.") |
| 3826 | (license license:gpl3))) |
| 3827 | |
| 3828 | (define-public r-gcrma |
| 3829 | (package |
| 3830 | (name "r-gcrma") |
| 3831 | (version "2.54.0") |
| 3832 | (source |
| 3833 | (origin |
| 3834 | (method url-fetch) |
| 3835 | (uri (bioconductor-uri "gcrma" version)) |
| 3836 | (sha256 |
| 3837 | (base32 |
| 3838 | "1v5fi98gdmj002ryq0rgsg2l4x3m3w5pz4h3bx4v8lk15azafgim")))) |
| 3839 | (build-system r-build-system) |
| 3840 | (propagated-inputs |
| 3841 | `(("r-affy" ,r-affy) |
| 3842 | ("r-affyio" ,r-affyio) |
| 3843 | ("r-biobase" ,r-biobase) |
| 3844 | ("r-biocmanager" ,r-biocmanager) |
| 3845 | ("r-biostrings" ,r-biostrings) |
| 3846 | ("r-xvector" ,r-xvector))) |
| 3847 | (home-page "https://bioconductor.org/packages/gcrma/") |
| 3848 | (synopsis "Background adjustment using sequence information") |
| 3849 | (description |
| 3850 | "Gcrma adjusts for background intensities in Affymetrix array data which |
| 3851 | include optical noise and @dfn{non-specific binding} (NSB). The main function |
| 3852 | @code{gcrma} converts background adjusted probe intensities to expression |
| 3853 | measures using the same normalization and summarization methods as a |
| 3854 | @dfn{Robust Multiarray Average} (RMA). Gcrma uses probe sequence information |
| 3855 | to estimate probe affinity to NSB. The sequence information is summarized in |
| 3856 | a more complex way than the simple GC content. Instead, the base types (A, T, |
| 3857 | G or C) at each position along the probe determine the affinity of each probe. |
| 3858 | The parameters of the position-specific base contributions to the probe |
| 3859 | affinity is estimated in an NSB experiment in which only NSB but no |
| 3860 | gene-specific bidning is expected.") |
| 3861 | ;; Any version of the LGPL |
| 3862 | (license license:lgpl2.1+))) |
| 3863 | |
| 3864 | (define-public r-simpleaffy |
| 3865 | (package |
| 3866 | (name "r-simpleaffy") |
| 3867 | (version "2.58.0") |
| 3868 | (source |
| 3869 | (origin |
| 3870 | (method url-fetch) |
| 3871 | (uri (bioconductor-uri "simpleaffy" version)) |
| 3872 | (sha256 |
| 3873 | (base32 |
| 3874 | "0bry0d2vw0w2rrpnmfm1kl5v4rdclypmy33jvs9l43vd6vx2ra9s")))) |
| 3875 | (build-system r-build-system) |
| 3876 | (propagated-inputs |
| 3877 | `(("r-affy" ,r-affy) |
| 3878 | ("r-biobase" ,r-biobase) |
| 3879 | ("r-biocgenerics" ,r-biocgenerics) |
| 3880 | ("r-gcrma" ,r-gcrma) |
| 3881 | ("r-genefilter" ,r-genefilter))) |
| 3882 | (home-page "https://bioconductor.org/packages/simpleaffy/") |
| 3883 | (synopsis "Very simple high level analysis of Affymetrix data") |
| 3884 | (description |
| 3885 | "This package provides high level functions for reading Affy @file{.CEL} |
| 3886 | files, phenotypic data, and then computing simple things with it, such as |
| 3887 | t-tests, fold changes and the like. It makes heavy use of the @code{affy} |
| 3888 | library. It also has some basic scatter plot functions and mechanisms for |
| 3889 | generating high resolution journal figures.") |
| 3890 | (license license:gpl2+))) |
| 3891 | |
| 3892 | (define-public r-yaqcaffy |
| 3893 | (package |
| 3894 | (name "r-yaqcaffy") |
| 3895 | (version "1.42.0") |
| 3896 | (source |
| 3897 | (origin |
| 3898 | (method url-fetch) |
| 3899 | (uri (bioconductor-uri "yaqcaffy" version)) |
| 3900 | (sha256 |
| 3901 | (base32 |
| 3902 | "192n1zvd54nm9q71vyb6dcr7ia6givf4bjwf6542jjig085lwhxk")))) |
| 3903 | (build-system r-build-system) |
| 3904 | (propagated-inputs |
| 3905 | `(("r-simpleaffy" ,r-simpleaffy))) |
| 3906 | (home-page "https://bioconductor.org/packages/yaqcaffy/") |
| 3907 | (synopsis "Affymetrix quality control and reproducibility analysis") |
| 3908 | (description |
| 3909 | "This is a package that can be used for quality control of Affymetrix |
| 3910 | GeneChip expression data and reproducibility analysis of human whole genome |
| 3911 | chips with the MAQC reference datasets.") |
| 3912 | (license license:artistic2.0))) |
| 3913 | |
| 3914 | (define-public r-quantro |
| 3915 | (package |
| 3916 | (name "r-quantro") |
| 3917 | (version "1.16.0") |
| 3918 | (source |
| 3919 | (origin |
| 3920 | (method url-fetch) |
| 3921 | (uri (bioconductor-uri "quantro" version)) |
| 3922 | (sha256 |
| 3923 | (base32 |
| 3924 | "1777gjgn855f04yv7hx70h9l8idmjzamkpazaq2cdr8qzhxwy2ib")))) |
| 3925 | (build-system r-build-system) |
| 3926 | (propagated-inputs |
| 3927 | `(("r-biobase" ,r-biobase) |
| 3928 | ("r-doparallel" ,r-doparallel) |
| 3929 | ("r-foreach" ,r-foreach) |
| 3930 | ("r-ggplot2" ,r-ggplot2) |
| 3931 | ("r-iterators" ,r-iterators) |
| 3932 | ("r-minfi" ,r-minfi) |
| 3933 | ("r-rcolorbrewer" ,r-rcolorbrewer))) |
| 3934 | (home-page "https://bioconductor.org/packages/quantro/") |
| 3935 | (synopsis "Test for when to use quantile normalization") |
| 3936 | (description |
| 3937 | "This package provides a data-driven test for the assumptions of quantile |
| 3938 | normalization using raw data such as objects that inherit eSets (e.g. |
| 3939 | ExpressionSet, MethylSet). Group level information about each sample (such as |
| 3940 | Tumor / Normal status) must also be provided because the test assesses if |
| 3941 | there are global differences in the distributions between the user-defined |
| 3942 | groups.") |
| 3943 | (license license:gpl3+))) |
| 3944 | |
| 3945 | (define-public r-yarn |
| 3946 | (package |
| 3947 | (name "r-yarn") |
| 3948 | (version "1.8.1") |
| 3949 | (source |
| 3950 | (origin |
| 3951 | (method url-fetch) |
| 3952 | (uri (bioconductor-uri "yarn" version)) |
| 3953 | (sha256 |
| 3954 | (base32 |
| 3955 | "0c84x1zq34hadpsyaa873r8kg0jcxp09c2z63377hlmhsll90l7s")))) |
| 3956 | (build-system r-build-system) |
| 3957 | (propagated-inputs |
| 3958 | `(("r-biobase" ,r-biobase) |
| 3959 | ("r-biomart" ,r-biomart) |
| 3960 | ("r-downloader" ,r-downloader) |
| 3961 | ("r-edger" ,r-edger) |
| 3962 | ("r-gplots" ,r-gplots) |
| 3963 | ("r-limma" ,r-limma) |
| 3964 | ("r-matrixstats" ,r-matrixstats) |
| 3965 | ("r-preprocesscore" ,r-preprocesscore) |
| 3966 | ("r-quantro" ,r-quantro) |
| 3967 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 3968 | ("r-readr" ,r-readr))) |
| 3969 | (home-page "https://bioconductor.org/packages/yarn/") |
| 3970 | (synopsis "Robust multi-condition RNA-Seq preprocessing and normalization") |
| 3971 | (description |
| 3972 | "Expedite large RNA-Seq analyses using a combination of previously |
| 3973 | developed tools. YARN is meant to make it easier for the user in performing |
| 3974 | basic mis-annotation quality control, filtering, and condition-aware |
| 3975 | normalization. YARN leverages many Bioconductor tools and statistical |
| 3976 | techniques to account for the large heterogeneity and sparsity found in very |
| 3977 | large RNA-seq experiments.") |
| 3978 | (license license:artistic2.0))) |
| 3979 | |
| 3980 | (define-public r-roar |
| 3981 | (package |
| 3982 | (name "r-roar") |
| 3983 | (version "1.18.0") |
| 3984 | (source |
| 3985 | (origin |
| 3986 | (method url-fetch) |
| 3987 | (uri (bioconductor-uri "roar" version)) |
| 3988 | (sha256 |
| 3989 | (base32 |
| 3990 | "15650s9vs7dvmqpvrs4xwn6j4kh14yqsx4daqyhhxxr68kn8mklw")))) |
| 3991 | (build-system r-build-system) |
| 3992 | (propagated-inputs |
| 3993 | `(("r-biocgenerics" ,r-biocgenerics) |
| 3994 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 3995 | ("r-genomicalignments" ,r-genomicalignments) |
| 3996 | ("r-genomicranges" ,r-genomicranges) |
| 3997 | ("r-iranges" ,r-iranges) |
| 3998 | ("r-rtracklayer" ,r-rtracklayer) |
| 3999 | ("r-s4vectors" ,r-s4vectors) |
| 4000 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 4001 | (home-page "https://github.com/vodkatad/roar/") |
| 4002 | (synopsis "Identify differential APA usage from RNA-seq alignments") |
| 4003 | (description |
| 4004 | "This package provides tools for identifying preferential usage of APA |
| 4005 | sites, comparing two biological conditions, starting from known alternative |
| 4006 | sites and alignments obtained from standard RNA-seq experiments.") |
| 4007 | (license license:gpl3))) |
| 4008 | |
| 4009 | (define-public r-xbseq |
| 4010 | (package |
| 4011 | (name "r-xbseq") |
| 4012 | (version "1.14.1") |
| 4013 | (source |
| 4014 | (origin |
| 4015 | (method url-fetch) |
| 4016 | (uri (bioconductor-uri "XBSeq" version)) |
| 4017 | (sha256 |
| 4018 | (base32 |
| 4019 | "0na0jiqfy40bzl243gqc2214k4hibv6v4ndiqwq0c5f78cyr6lph")))) |
| 4020 | (properties `((upstream-name . "XBSeq"))) |
| 4021 | (build-system r-build-system) |
| 4022 | (propagated-inputs |
| 4023 | `(("r-biobase" ,r-biobase) |
| 4024 | ("r-deseq2" ,r-deseq2) |
| 4025 | ("r-dplyr" ,r-dplyr) |
| 4026 | ("r-ggplot2" ,r-ggplot2) |
| 4027 | ("r-locfit" ,r-locfit) |
| 4028 | ("r-magrittr" ,r-magrittr) |
| 4029 | ("r-matrixstats" ,r-matrixstats) |
| 4030 | ("r-pracma" ,r-pracma) |
| 4031 | ("r-roar" ,r-roar))) |
| 4032 | (home-page "https://github.com/Liuy12/XBSeq") |
| 4033 | (synopsis "Test for differential expression for RNA-seq data") |
| 4034 | (description |
| 4035 | "XBSeq is a novel algorithm for testing RNA-seq @dfn{differential |
| 4036 | expression} (DE), where a statistical model was established based on the |
| 4037 | assumption that observed signals are the convolution of true expression |
| 4038 | signals and sequencing noises. The mapped reads in non-exonic regions are |
| 4039 | considered as sequencing noises, which follows a Poisson distribution. Given |
| 4040 | measurable observed signal and background noise from RNA-seq data, true |
| 4041 | expression signals, assuming governed by the negative binomial distribution, |
| 4042 | can be delineated and thus the accurate detection of differential expressed |
| 4043 | genes.") |
| 4044 | (license license:gpl3+))) |
| 4045 | |
| 4046 | (define-public r-massspecwavelet |
| 4047 | (package |
| 4048 | (name "r-massspecwavelet") |
| 4049 | (version "1.48.1") |
| 4050 | (source |
| 4051 | (origin |
| 4052 | (method url-fetch) |
| 4053 | (uri (bioconductor-uri "MassSpecWavelet" version)) |
| 4054 | (sha256 |
| 4055 | (base32 |
| 4056 | "1xcr568a36b570rldy27wq4a2jn7yf5f6fddlzgx6x944jdn3ckz")))) |
| 4057 | (properties |
| 4058 | `((upstream-name . "MassSpecWavelet"))) |
| 4059 | (build-system r-build-system) |
| 4060 | (propagated-inputs |
| 4061 | `(("r-waveslim" ,r-waveslim))) |
| 4062 | (home-page "https://bioconductor.org/packages/MassSpecWavelet/") |
| 4063 | (synopsis "Mass spectrum processing by wavelet-based algorithms") |
| 4064 | (description |
| 4065 | "The MassSpecWavelet package aims to process @dfn{Mass Spectrometry} (MS) |
| 4066 | data mainly through the use of wavelet transforms. It supports peak detection |
| 4067 | based on @dfn{Continuous Wavelet Transform} (CWT).") |
| 4068 | (license license:lgpl2.0+))) |
| 4069 | |
| 4070 | (define-public r-xcms |
| 4071 | (package |
| 4072 | (name "r-xcms") |
| 4073 | (version "3.4.4") |
| 4074 | (source |
| 4075 | (origin |
| 4076 | (method url-fetch) |
| 4077 | (uri (bioconductor-uri "xcms" version)) |
| 4078 | (sha256 |
| 4079 | (base32 |
| 4080 | "073f25m7y8z4560k93d99fv72pr7nrgrp054zssi7jhas4l3ddww")))) |
| 4081 | (build-system r-build-system) |
| 4082 | (propagated-inputs |
| 4083 | `(("r-biobase" ,r-biobase) |
| 4084 | ("r-biocgenerics" ,r-biocgenerics) |
| 4085 | ("r-biocparallel" ,r-biocparallel) |
| 4086 | ("r-lattice" ,r-lattice) |
| 4087 | ("r-massspecwavelet" ,r-massspecwavelet) |
| 4088 | ("r-msnbase" ,r-msnbase) |
| 4089 | ("r-multtest" ,r-multtest) |
| 4090 | ("r-mzr" ,r-mzr) |
| 4091 | ("r-plyr" ,r-plyr) |
| 4092 | ("r-protgenerics" ,r-protgenerics) |
| 4093 | ("r-rann" ,r-rann) |
| 4094 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 4095 | ("r-robustbase" ,r-robustbase) |
| 4096 | ("r-s4vectors" ,r-s4vectors))) |
| 4097 | (home-page "https://bioconductor.org/packages/xcms/") |
| 4098 | (synopsis "LC/MS and GC/MS mass spectrometry data analysis") |
| 4099 | (description |
| 4100 | "This package provides a framework for processing and visualization of |
| 4101 | chromatographically separated and single-spectra mass spectral data. It |
| 4102 | imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. It preprocesses |
| 4103 | data for high-throughput, untargeted analyte profiling.") |
| 4104 | (license license:gpl2+))) |
| 4105 | |
| 4106 | (define-public r-wrench |
| 4107 | (package |
| 4108 | (name "r-wrench") |
| 4109 | (version "1.0.0") |
| 4110 | (source |
| 4111 | (origin |
| 4112 | (method url-fetch) |
| 4113 | (uri (bioconductor-uri "Wrench" version)) |
| 4114 | (sha256 |
| 4115 | (base32 |
| 4116 | "12gfdj2p52pah67bimz14xcwmcb4c2snjwswj0fns7v3v1h9rlqg")))) |
| 4117 | (properties `((upstream-name . "Wrench"))) |
| 4118 | (build-system r-build-system) |
| 4119 | (propagated-inputs |
| 4120 | `(("r-limma" ,r-limma) |
| 4121 | ("r-locfit" ,r-locfit) |
| 4122 | ("r-matrixstats" ,r-matrixstats))) |
| 4123 | (home-page "https://github.com/HCBravoLab/Wrench") |
| 4124 | (synopsis "Wrench normalization for sparse count data") |
| 4125 | (description |
| 4126 | "Wrench is a package for normalization sparse genomic count data, like |
| 4127 | that arising from 16s metagenomic surveys.") |
| 4128 | (license license:artistic2.0))) |
| 4129 | |
| 4130 | (define-public r-wiggleplotr |
| 4131 | (package |
| 4132 | (name "r-wiggleplotr") |
| 4133 | (version "1.6.1") |
| 4134 | (source |
| 4135 | (origin |
| 4136 | (method url-fetch) |
| 4137 | (uri (bioconductor-uri "wiggleplotr" version)) |
| 4138 | (sha256 |
| 4139 | (base32 |
| 4140 | "12fhbskkjwv4d9bdy3gab8n9pcf7qpwiwgx0248as445vfw8dil3")))) |
| 4141 | (build-system r-build-system) |
| 4142 | (propagated-inputs |
| 4143 | `(("r-assertthat" ,r-assertthat) |
| 4144 | ("r-cowplot" ,r-cowplot) |
| 4145 | ("r-dplyr" ,r-dplyr) |
| 4146 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 4147 | ("r-genomicranges" ,r-genomicranges) |
| 4148 | ("r-ggplot2" ,r-ggplot2) |
| 4149 | ("r-iranges" ,r-iranges) |
| 4150 | ("r-purrr" ,r-purrr) |
| 4151 | ("r-rtracklayer" ,r-rtracklayer) |
| 4152 | ("r-s4vectors" ,r-s4vectors))) |
| 4153 | (home-page "https://bioconductor.org/packages/wiggleplotr/") |
| 4154 | (synopsis "Make read coverage plots from BigWig files") |
| 4155 | (description |
| 4156 | "This package provides tools to visualize read coverage from sequencing |
| 4157 | experiments together with genomic annotations (genes, transcripts, peaks). |
| 4158 | Introns of long transcripts can be rescaled to a fixed length for better |
| 4159 | visualization of exonic read coverage.") |
| 4160 | (license license:asl2.0))) |
| 4161 | |
| 4162 | (define-public r-widgettools |
| 4163 | (package |
| 4164 | (name "r-widgettools") |
| 4165 | (version "1.60.0") |
| 4166 | (source |
| 4167 | (origin |
| 4168 | (method url-fetch) |
| 4169 | (uri (bioconductor-uri "widgetTools" version)) |
| 4170 | (sha256 |
| 4171 | (base32 |
| 4172 | "0mz69pdr6q69avsvs6r5ncdkdmgwfislpil4v18dsflw4j454gwf")))) |
| 4173 | (properties `((upstream-name . "widgetTools"))) |
| 4174 | (build-system r-build-system) |
| 4175 | (home-page "https://bioconductor.org/packages/widgetTools/") |
| 4176 | (synopsis "Tools for creating interactive tcltk widgets") |
| 4177 | (description |
| 4178 | "This packages contains tools to support the construction of tcltk |
| 4179 | widgets in R.") |
| 4180 | ;; Any version of the LGPL. |
| 4181 | (license license:lgpl3+))) |
| 4182 | |
| 4183 | (define-public r-webbioc |
| 4184 | (package |
| 4185 | (name "r-webbioc") |
| 4186 | (version "1.54.0") |
| 4187 | (source |
| 4188 | (origin |
| 4189 | (method url-fetch) |
| 4190 | (uri (bioconductor-uri "webbioc" version)) |
| 4191 | (sha256 |
| 4192 | (base32 |
| 4193 | "16n6wc9q51wfpmh9y77p53sqdqdd8pn50c67vf6h4n7gv5wgnpwi")))) |
| 4194 | (build-system r-build-system) |
| 4195 | (inputs |
| 4196 | `(("netpbm" ,netpbm) |
| 4197 | ("perl" ,perl))) |
| 4198 | (propagated-inputs |
| 4199 | `(("r-affy" ,r-affy) |
| 4200 | ("r-annaffy" ,r-annaffy) |
| 4201 | ("r-biobase" ,r-biobase) |
| 4202 | ("r-biocmanager" ,r-biocmanager) |
| 4203 | ("r-gcrma" ,r-gcrma) |
| 4204 | ("r-multtest" ,r-multtest) |
| 4205 | ("r-qvalue" ,r-qvalue) |
| 4206 | ("r-vsn" ,r-vsn))) |
| 4207 | (home-page "https://www.bioconductor.org/") |
| 4208 | (synopsis "Bioconductor web interface") |
| 4209 | (description |
| 4210 | "This package provides an integrated web interface for doing microarray |
| 4211 | analysis using several of the Bioconductor packages. It is intended to be |
| 4212 | deployed as a centralized bioinformatics resource for use by many users. |
| 4213 | Currently only Affymetrix oligonucleotide analysis is supported.") |
| 4214 | (license license:gpl2+))) |
| 4215 | |
| 4216 | (define-public r-zfpkm |
| 4217 | (package |
| 4218 | (name "r-zfpkm") |
| 4219 | (version "1.4.1") |
| 4220 | (source |
| 4221 | (origin |
| 4222 | (method url-fetch) |
| 4223 | (uri (bioconductor-uri "zFPKM" version)) |
| 4224 | (sha256 |
| 4225 | (base32 |
| 4226 | "0rvfrjxxvfng9fxxn316gm96v4rahx62vlk3axr2bzjbi1r4s8v5")))) |
| 4227 | (properties `((upstream-name . "zFPKM"))) |
| 4228 | (build-system r-build-system) |
| 4229 | (propagated-inputs |
| 4230 | `(("r-checkmate" ,r-checkmate) |
| 4231 | ("r-dplyr" ,r-dplyr) |
| 4232 | ("r-ggplot2" ,r-ggplot2) |
| 4233 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 4234 | ("r-tidyr" ,r-tidyr))) |
| 4235 | (home-page "https://github.com/ronammar/zFPKM/") |
| 4236 | (synopsis "Functions to facilitate zFPKM transformations") |
| 4237 | (description |
| 4238 | "This is a package to perform the zFPKM transform on RNA-seq FPKM data. |
| 4239 | This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID |
| 4240 | 24215113).") |
| 4241 | (license license:gpl3))) |
| 4242 | |
| 4243 | (define-public r-rbowtie2 |
| 4244 | (package |
| 4245 | (name "r-rbowtie2") |
| 4246 | (version "1.4.0") |
| 4247 | (source |
| 4248 | (origin |
| 4249 | (method url-fetch) |
| 4250 | (uri (bioconductor-uri "Rbowtie2" version)) |
| 4251 | (sha256 |
| 4252 | (base32 |
| 4253 | "045cmfwqzcj4zn6r16hkpmr5sd5y0mxvrs5yynf460fdz2p418cr")))) |
| 4254 | (properties `((upstream-name . "Rbowtie2"))) |
| 4255 | (build-system r-build-system) |
| 4256 | (inputs |
| 4257 | `(("zlib" ,zlib))) |
| 4258 | (home-page "https://bioconductor.org/packages/Rbowtie2/") |
| 4259 | (synopsis "R wrapper for Bowtie2 and AdapterRemoval") |
| 4260 | (description |
| 4261 | "This package provides an R wrapper of the popular @code{bowtie2} |
| 4262 | sequencing reads aligner and @code{AdapterRemoval}, a convenient tool for |
| 4263 | rapid adapter trimming, identification, and read merging.") |
| 4264 | (license license:gpl3+))) |
| 4265 | |
| 4266 | (define-public r-progeny |
| 4267 | (package |
| 4268 | (name "r-progeny") |
| 4269 | (version "1.4.1") |
| 4270 | (source |
| 4271 | (origin |
| 4272 | (method url-fetch) |
| 4273 | (uri (bioconductor-uri "progeny" version)) |
| 4274 | (sha256 |
| 4275 | (base32 |
| 4276 | "02z09rbzi305jrwzai8zayxi82563lxcaldp4r9pw564qkbl7pk7")))) |
| 4277 | (build-system r-build-system) |
| 4278 | (propagated-inputs `(("r-biobase" ,r-biobase))) |
| 4279 | (home-page "https://github.com/saezlab/progeny") |
| 4280 | (synopsis "Pathway responsive gene activity inference") |
| 4281 | (description |
| 4282 | "This package provides a function to infer pathway activity from gene |
| 4283 | expression. It contains the linear model inferred in the publication |
| 4284 | \"Perturbation-response genes reveal signaling footprints in cancer gene |
| 4285 | expression\".") |
| 4286 | (license license:asl2.0))) |
| 4287 | |
| 4288 | (define-public r-arrmnormalization |
| 4289 | (package |
| 4290 | (name "r-arrmnormalization") |
| 4291 | (version "1.22.0") |
| 4292 | (source |
| 4293 | (origin |
| 4294 | (method url-fetch) |
| 4295 | (uri (bioconductor-uri "ARRmNormalization" version)) |
| 4296 | (sha256 |
| 4297 | (base32 |
| 4298 | "09wfd4vqfvmkpqn9dwqly1dz4h1ckh621jbwj1dab6q4z0dfmzmd")))) |
| 4299 | (properties |
| 4300 | `((upstream-name . "ARRmNormalization"))) |
| 4301 | (build-system r-build-system) |
| 4302 | (propagated-inputs `(("r-arrmdata" ,r-arrmdata))) |
| 4303 | (home-page "https://bioconductor.org/packages/ARRmNormalization/") |
| 4304 | (synopsis "Adaptive robust regression normalization for methylation data") |
| 4305 | (description |
| 4306 | "This is a package to perform the @dfn{Adaptive Robust Regression |
| 4307 | method} (ARRm) for the normalization of methylation data from the Illumina |
| 4308 | Infinium HumanMethylation 450k assay.") |
| 4309 | (license license:artistic2.0))) |
| 4310 | |
| 4311 | (define-public r-biocfilecache |
| 4312 | (package |
| 4313 | (name "r-biocfilecache") |
| 4314 | (version "1.8.0") |
| 4315 | (source |
| 4316 | (origin |
| 4317 | (method url-fetch) |
| 4318 | (uri (bioconductor-uri "BiocFileCache" version)) |
| 4319 | (sha256 |
| 4320 | (base32 |
| 4321 | "1mi8p8hvrdxim8lqsid2cb7284imyjf9rlzsrdlzdjac7dp9bpdb")))) |
| 4322 | (properties `((upstream-name . "BiocFileCache"))) |
| 4323 | (build-system r-build-system) |
| 4324 | (propagated-inputs |
| 4325 | `(("r-curl" ,r-curl) |
| 4326 | ("r-dbi" ,r-dbi) |
| 4327 | ("r-dbplyr" ,r-dbplyr) |
| 4328 | ("r-dplyr" ,r-dplyr) |
| 4329 | ("r-httr" ,r-httr) |
| 4330 | ("r-rappdirs" ,r-rappdirs) |
| 4331 | ("r-rsqlite" ,r-rsqlite))) |
| 4332 | (home-page "https://bioconductor.org/packages/BiocFileCache/") |
| 4333 | (synopsis "Manage files across sessions") |
| 4334 | (description |
| 4335 | "This package creates a persistent on-disk cache of files that the user |
| 4336 | can add, update, and retrieve. It is useful for managing resources (such as |
| 4337 | custom Txdb objects) that are costly or difficult to create, web resources, |
| 4338 | and data files used across sessions.") |
| 4339 | (license license:artistic2.0))) |