| 1 | ;;; GNU Guix --- Functional package management for GNU |
| 2 | ;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net> |
| 3 | ;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org> |
| 4 | ;;; Copyright © 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 graph) |
| 31 | #:use-module (gnu packages maths) |
| 32 | #:use-module (gnu packages statistics) |
| 33 | #:use-module (gnu packages web)) |
| 34 | |
| 35 | (define-public r-bsgenome-dmelanogaster-ucsc-dm6 |
| 36 | (package |
| 37 | (name "r-bsgenome-dmelanogaster-ucsc-dm6") |
| 38 | (version "1.4.1") |
| 39 | (source (origin |
| 40 | (method url-fetch) |
| 41 | ;; We cannot use bioconductor-uri here because this tarball is |
| 42 | ;; located under "data/annotation/" instead of "bioc/". |
| 43 | (uri (string-append "https://www.bioconductor.org/packages/" |
| 44 | "release/data/annotation/src/contrib/" |
| 45 | "BSgenome.Dmelanogaster.UCSC.dm6_" |
| 46 | version ".tar.gz")) |
| 47 | (sha256 |
| 48 | (base32 |
| 49 | "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060")))) |
| 50 | (properties |
| 51 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6"))) |
| 52 | (build-system r-build-system) |
| 53 | ;; As this package provides little more than a very large data file it |
| 54 | ;; doesn't make sense to build substitutes. |
| 55 | (arguments `(#:substitutable? #f)) |
| 56 | (propagated-inputs |
| 57 | `(("r-bsgenome" ,r-bsgenome))) |
| 58 | (home-page |
| 59 | "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/") |
| 60 | (synopsis "Full genome sequences for Fly") |
| 61 | (description |
| 62 | "This package provides full genome sequences for Drosophila |
| 63 | melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings |
| 64 | objects.") |
| 65 | (license license:artistic2.0))) |
| 66 | |
| 67 | (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked |
| 68 | (package |
| 69 | (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked") |
| 70 | (version "1.3.99") |
| 71 | (source (origin |
| 72 | (method url-fetch) |
| 73 | ;; We cannot use bioconductor-uri here because this tarball is |
| 74 | ;; located under "data/annotation/" instead of "bioc/". |
| 75 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 76 | "release/data/annotation/src/contrib/" |
| 77 | "BSgenome.Dmelanogaster.UCSC.dm3.masked_" |
| 78 | version ".tar.gz")) |
| 79 | (sha256 |
| 80 | (base32 |
| 81 | "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap")))) |
| 82 | (properties |
| 83 | `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked"))) |
| 84 | (build-system r-build-system) |
| 85 | (propagated-inputs |
| 86 | `(("r-bsgenome" ,r-bsgenome) |
| 87 | ("r-bsgenome-dmelanogaster-ucsc-dm3" |
| 88 | ,r-bsgenome-dmelanogaster-ucsc-dm3))) |
| 89 | (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/") |
| 90 | (synopsis "Full masked genome sequences for Fly") |
| 91 | (description |
| 92 | "This package provides full masked genome sequences for Drosophila |
| 93 | melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in |
| 94 | Biostrings objects. The sequences are the same as in |
| 95 | BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following |
| 96 | masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of |
| 97 | intra-contig ambiguities (AMB mask), (3) the mask of repeats from |
| 98 | RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats |
| 99 | Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by default.") |
| 100 | (license license:artistic2.0))) |
| 101 | |
| 102 | (define-public r-bsgenome-hsapiens-ucsc-hg19-masked |
| 103 | (package |
| 104 | (name "r-bsgenome-hsapiens-ucsc-hg19-masked") |
| 105 | (version "1.3.99") |
| 106 | (source (origin |
| 107 | (method url-fetch) |
| 108 | ;; We cannot use bioconductor-uri here because this tarball is |
| 109 | ;; located under "data/annotation/" instead of "bioc/". |
| 110 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 111 | "release/data/annotation/src/contrib/" |
| 112 | "BSgenome.Hsapiens.UCSC.hg19.masked_" |
| 113 | version ".tar.gz")) |
| 114 | (sha256 |
| 115 | (base32 |
| 116 | "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr")))) |
| 117 | (properties |
| 118 | `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked"))) |
| 119 | (build-system r-build-system) |
| 120 | (propagated-inputs |
| 121 | `(("r-bsgenome" ,r-bsgenome) |
| 122 | ("r-bsgenome-hsapiens-ucsc-hg19" |
| 123 | ,r-bsgenome-hsapiens-ucsc-hg19))) |
| 124 | (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/") |
| 125 | (synopsis "Full masked genome sequences for Homo sapiens") |
| 126 | (description |
| 127 | "This package provides full genome sequences for Homo sapiens (Human) as |
| 128 | provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The |
| 129 | sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of |
| 130 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS |
| 131 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of |
| 132 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem |
| 133 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by |
| 134 | default.") |
| 135 | (license license:artistic2.0))) |
| 136 | |
| 137 | (define-public r-bsgenome-mmusculus-ucsc-mm9-masked |
| 138 | (package |
| 139 | (name "r-bsgenome-mmusculus-ucsc-mm9-masked") |
| 140 | (version "1.3.99") |
| 141 | (source (origin |
| 142 | (method url-fetch) |
| 143 | ;; We cannot use bioconductor-uri here because this tarball is |
| 144 | ;; located under "data/annotation/" instead of "bioc/". |
| 145 | (uri (string-append "http://www.bioconductor.org/packages/" |
| 146 | "release/data/annotation/src/contrib/" |
| 147 | "BSgenome.Mmusculus.UCSC.mm9.masked_" |
| 148 | version ".tar.gz")) |
| 149 | (sha256 |
| 150 | (base32 |
| 151 | "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn")))) |
| 152 | (properties |
| 153 | `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked"))) |
| 154 | (build-system r-build-system) |
| 155 | (propagated-inputs |
| 156 | `(("r-bsgenome" ,r-bsgenome) |
| 157 | ("r-bsgenome-mmusculus-ucsc-mm9" |
| 158 | ,r-bsgenome-mmusculus-ucsc-mm9))) |
| 159 | (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/") |
| 160 | (synopsis "Full masked genome sequences for Mouse") |
| 161 | (description |
| 162 | "This package provides full genome sequences for Mus musculus (Mouse) as |
| 163 | provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The |
| 164 | sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of |
| 165 | them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS |
| 166 | mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of |
| 167 | repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem |
| 168 | Repeats Finder (TRF mask). Only the AGAPS and AMB masks are \"active\" by |
| 169 | default." ) |
| 170 | (license license:artistic2.0))) |
| 171 | |
| 172 | (define-public r-genelendatabase |
| 173 | (package |
| 174 | (name "r-genelendatabase") |
| 175 | (version "1.16.0") |
| 176 | (source |
| 177 | (origin |
| 178 | (method url-fetch) |
| 179 | ;; We cannot use bioconductor-uri here because this tarball is |
| 180 | ;; located under "data/experiment/" instead of "bioc/". |
| 181 | (uri (string-append "https://bioconductor.org/packages/" |
| 182 | "release/data/experiment/src/contrib" |
| 183 | "/geneLenDataBase_" version ".tar.gz")) |
| 184 | (sha256 |
| 185 | (base32 |
| 186 | "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5")))) |
| 187 | (properties |
| 188 | `((upstream-name . "geneLenDataBase"))) |
| 189 | (build-system r-build-system) |
| 190 | (propagated-inputs |
| 191 | `(("r-rtracklayer" ,r-rtracklayer) |
| 192 | ("r-genomicfeatures" ,r-genomicfeatures))) |
| 193 | (home-page "https://bioconductor.org/packages/geneLenDataBase/") |
| 194 | (synopsis "Lengths of mRNA transcripts for a number of genomes") |
| 195 | (description |
| 196 | "This package provides the lengths of mRNA transcripts for a number of |
| 197 | genomes and gene ID formats, largely based on the UCSC table browser.") |
| 198 | (license license:lgpl2.0+))) |
| 199 | |
| 200 | (define-public r-txdb-mmusculus-ucsc-mm9-knowngene |
| 201 | (package |
| 202 | (name "r-txdb-mmusculus-ucsc-mm9-knowngene") |
| 203 | (version "3.2.2") |
| 204 | (source (origin |
| 205 | (method url-fetch) |
| 206 | ;; We cannot use bioconductor-uri here because this tarball is |
| 207 | ;; located under "data/annotation/" instead of "bioc/". |
| 208 | (uri (string-append "https://bioconductor.org/packages/" |
| 209 | "release/data/annotation/src/contrib" |
| 210 | "/TxDb.Mmusculus.UCSC.mm9.knownGene_" |
| 211 | version ".tar.gz")) |
| 212 | (sha256 |
| 213 | (base32 |
| 214 | "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2")))) |
| 215 | (properties |
| 216 | `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene"))) |
| 217 | (build-system r-build-system) |
| 218 | (propagated-inputs |
| 219 | `(("r-genomicfeatures" ,r-genomicfeatures) |
| 220 | ("r-annotationdbi" ,r-annotationdbi))) |
| 221 | (home-page |
| 222 | "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/") |
| 223 | (synopsis "Annotation package for mouse genome in TxDb format") |
| 224 | (description |
| 225 | "This package provides an annotation database of Mouse genome data. It |
| 226 | is derived from the UCSC mm9 genome and based on the \"knownGene\" track. The |
| 227 | database is exposed as a @code{TxDb} object.") |
| 228 | (license license:artistic2.0))) |
| 229 | |
| 230 | \f |
| 231 | (define-public r-annotate |
| 232 | (package |
| 233 | (name "r-annotate") |
| 234 | (version "1.60.0") |
| 235 | (source |
| 236 | (origin |
| 237 | (method url-fetch) |
| 238 | (uri (bioconductor-uri "annotate" version)) |
| 239 | (sha256 |
| 240 | (base32 |
| 241 | "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n")))) |
| 242 | (build-system r-build-system) |
| 243 | (propagated-inputs |
| 244 | `(("r-annotationdbi" ,r-annotationdbi) |
| 245 | ("r-biobase" ,r-biobase) |
| 246 | ("r-biocgenerics" ,r-biocgenerics) |
| 247 | ("r-dbi" ,r-dbi) |
| 248 | ("r-rcurl" ,r-rcurl) |
| 249 | ("r-xml" ,r-xml) |
| 250 | ("r-xtable" ,r-xtable))) |
| 251 | (home-page |
| 252 | "https://bioconductor.org/packages/annotate") |
| 253 | (synopsis "Annotation for microarrays") |
| 254 | (description "This package provides R environments for the annotation of |
| 255 | microarrays.") |
| 256 | (license license:artistic2.0))) |
| 257 | |
| 258 | (define-public r-hpar |
| 259 | (package |
| 260 | (name "r-hpar") |
| 261 | (version "1.24.0") |
| 262 | (source |
| 263 | (origin |
| 264 | (method url-fetch) |
| 265 | (uri (bioconductor-uri "hpar" version)) |
| 266 | (sha256 |
| 267 | (base32 |
| 268 | "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn")))) |
| 269 | (build-system r-build-system) |
| 270 | (home-page "https://bioconductor.org/packages/hpar/") |
| 271 | (synopsis "Human Protein Atlas in R") |
| 272 | (description "This package provides a simple interface to and data from |
| 273 | the Human Protein Atlas project.") |
| 274 | (license license:artistic2.0))) |
| 275 | |
| 276 | (define-public r-regioner |
| 277 | (package |
| 278 | (name "r-regioner") |
| 279 | (version "1.14.0") |
| 280 | (source |
| 281 | (origin |
| 282 | (method url-fetch) |
| 283 | (uri (bioconductor-uri "regioneR" version)) |
| 284 | (sha256 |
| 285 | (base32 |
| 286 | "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd")))) |
| 287 | (properties `((upstream-name . "regioneR"))) |
| 288 | (build-system r-build-system) |
| 289 | (propagated-inputs |
| 290 | `(("r-biostrings" ,r-biostrings) |
| 291 | ("r-bsgenome" ,r-bsgenome) |
| 292 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 293 | ("r-genomicranges" ,r-genomicranges) |
| 294 | ("r-iranges" ,r-iranges) |
| 295 | ("r-memoise" ,r-memoise) |
| 296 | ("r-rtracklayer" ,r-rtracklayer) |
| 297 | ("r-s4vectors" ,r-s4vectors))) |
| 298 | (home-page "https://bioconductor.org/packages/regioneR/") |
| 299 | (synopsis "Association analysis of genomic regions") |
| 300 | (description "This package offers a statistical framework based on |
| 301 | customizable permutation tests to assess the association between genomic |
| 302 | region sets and other genomic features.") |
| 303 | (license license:artistic2.0))) |
| 304 | |
| 305 | (define-public r-diffbind |
| 306 | (package |
| 307 | (name "r-diffbind") |
| 308 | (version "2.10.0") |
| 309 | (source |
| 310 | (origin |
| 311 | (method url-fetch) |
| 312 | (uri (bioconductor-uri "DiffBind" version)) |
| 313 | (sha256 |
| 314 | (base32 |
| 315 | "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5")))) |
| 316 | (properties `((upstream-name . "DiffBind"))) |
| 317 | (build-system r-build-system) |
| 318 | (inputs |
| 319 | `(("zlib" ,zlib))) |
| 320 | (propagated-inputs |
| 321 | `(("r-amap" ,r-amap) |
| 322 | ("r-biocparallel" ,r-biocparallel) |
| 323 | ("r-deseq2" ,r-deseq2) |
| 324 | ("r-dplyr" ,r-dplyr) |
| 325 | ("r-edger" ,r-edger) |
| 326 | ("r-genomicalignments" ,r-genomicalignments) |
| 327 | ("r-genomicranges" ,r-genomicranges) |
| 328 | ("r-ggplot2" ,r-ggplot2) |
| 329 | ("r-ggrepel" ,r-ggrepel) |
| 330 | ("r-gplots" ,r-gplots) |
| 331 | ("r-iranges" ,r-iranges) |
| 332 | ("r-lattice" ,r-lattice) |
| 333 | ("r-limma" ,r-limma) |
| 334 | ("r-locfit" ,r-locfit) |
| 335 | ("r-rcolorbrewer" , r-rcolorbrewer) |
| 336 | ("r-rcpp" ,r-rcpp) |
| 337 | ("r-rsamtools" ,r-rsamtools) |
| 338 | ("r-s4vectors" ,r-s4vectors) |
| 339 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 340 | ("r-systempiper" ,r-systempiper) |
| 341 | ("r-zlibbioc" ,r-zlibbioc))) |
| 342 | (home-page "http://bioconductor.org/packages/DiffBind") |
| 343 | (synopsis "Differential binding analysis of ChIP-Seq peak data") |
| 344 | (description |
| 345 | "This package computes differentially bound sites from multiple |
| 346 | ChIP-seq experiments using affinity (quantitative) data. Also enables |
| 347 | occupancy (overlap) analysis and plotting functions.") |
| 348 | (license license:artistic2.0))) |
| 349 | |
| 350 | (define-public r-ripseeker |
| 351 | (package |
| 352 | (name "r-ripseeker") |
| 353 | (version "1.22.0") |
| 354 | (source |
| 355 | (origin |
| 356 | (method url-fetch) |
| 357 | (uri (bioconductor-uri "RIPSeeker" version)) |
| 358 | (sha256 |
| 359 | (base32 |
| 360 | "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i")))) |
| 361 | (properties `((upstream-name . "RIPSeeker"))) |
| 362 | (build-system r-build-system) |
| 363 | (propagated-inputs |
| 364 | `(("r-s4vectors" ,r-s4vectors) |
| 365 | ("r-iranges" ,r-iranges) |
| 366 | ("r-genomicranges" ,r-genomicranges) |
| 367 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 368 | ("r-rsamtools" ,r-rsamtools) |
| 369 | ("r-genomicalignments" ,r-genomicalignments) |
| 370 | ("r-rtracklayer" ,r-rtracklayer))) |
| 371 | (home-page "http://bioconductor.org/packages/RIPSeeker") |
| 372 | (synopsis |
| 373 | "Identifying protein-associated transcripts from RIP-seq experiments") |
| 374 | (description |
| 375 | "This package infers and discriminates RIP peaks from RIP-seq alignments |
| 376 | using two-state HMM with negative binomial emission probability. While |
| 377 | RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides |
| 378 | a suite of bioinformatics tools integrated within this self-contained software |
| 379 | package comprehensively addressing issues ranging from post-alignments |
| 380 | processing to visualization and annotation.") |
| 381 | (license license:gpl2))) |
| 382 | |
| 383 | (define-public r-multtest |
| 384 | (package |
| 385 | (name "r-multtest") |
| 386 | (version "2.38.0") |
| 387 | (source |
| 388 | (origin |
| 389 | (method url-fetch) |
| 390 | (uri (bioconductor-uri "multtest" version)) |
| 391 | (sha256 |
| 392 | (base32 |
| 393 | "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k")))) |
| 394 | (build-system r-build-system) |
| 395 | (propagated-inputs |
| 396 | `(("r-survival" ,r-survival) |
| 397 | ("r-biocgenerics" ,r-biocgenerics) |
| 398 | ("r-biobase" ,r-biobase) |
| 399 | ("r-mass" ,r-mass))) |
| 400 | (home-page "http://bioconductor.org/packages/multtest") |
| 401 | (synopsis "Resampling-based multiple hypothesis testing") |
| 402 | (description |
| 403 | "This package can do non-parametric bootstrap and permutation |
| 404 | resampling-based multiple testing procedures (including empirical Bayes |
| 405 | methods) for controlling the family-wise error rate (FWER), generalized |
| 406 | family-wise error rate (gFWER), tail probability of the proportion of |
| 407 | false positives (TPPFP), and false discovery rate (FDR). Several choices |
| 408 | of bootstrap-based null distribution are implemented (centered, centered |
| 409 | and scaled, quantile-transformed). Single-step and step-wise methods are |
| 410 | available. Tests based on a variety of T- and F-statistics (including |
| 411 | T-statistics based on regression parameters from linear and survival models |
| 412 | as well as those based on correlation parameters) are included. When probing |
| 413 | hypotheses with T-statistics, users may also select a potentially faster null |
| 414 | distribution which is multivariate normal with mean zero and variance |
| 415 | covariance matrix derived from the vector influence function. Results are |
| 416 | reported in terms of adjusted P-values, confidence regions and test statistic |
| 417 | cutoffs. The procedures are directly applicable to identifying differentially |
| 418 | expressed genes in DNA microarray experiments.") |
| 419 | (license license:lgpl3))) |
| 420 | |
| 421 | (define-public r-graph |
| 422 | (package |
| 423 | (name "r-graph") |
| 424 | (version "1.60.0") |
| 425 | (source (origin |
| 426 | (method url-fetch) |
| 427 | (uri (bioconductor-uri "graph" version)) |
| 428 | (sha256 |
| 429 | (base32 |
| 430 | "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i")))) |
| 431 | (build-system r-build-system) |
| 432 | (propagated-inputs |
| 433 | `(("r-biocgenerics" ,r-biocgenerics))) |
| 434 | (home-page "https://bioconductor.org/packages/graph") |
| 435 | (synopsis "Handle graph data structures in R") |
| 436 | (description |
| 437 | "This package implements some simple graph handling capabilities for R.") |
| 438 | (license license:artistic2.0))) |
| 439 | |
| 440 | (define-public r-codedepends |
| 441 | (package |
| 442 | (name "r-codedepends") |
| 443 | (version "0.6.5") |
| 444 | (source |
| 445 | (origin |
| 446 | (method url-fetch) |
| 447 | (uri (cran-uri "CodeDepends" version)) |
| 448 | (sha256 |
| 449 | (base32 |
| 450 | "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq")))) |
| 451 | (properties `((upstream-name . "CodeDepends"))) |
| 452 | (build-system r-build-system) |
| 453 | (propagated-inputs |
| 454 | `(("r-codetools" ,r-codetools) |
| 455 | ("r-graph" ,r-graph) |
| 456 | ("r-xml" ,r-xml))) |
| 457 | (home-page "http://cran.r-project.org/web/packages/CodeDepends") |
| 458 | (synopsis "Analysis of R code for reproducible research and code comprehension") |
| 459 | (description |
| 460 | "This package provides tools for analyzing R expressions or blocks of |
| 461 | code and determining the dependencies between them. It focuses on R scripts, |
| 462 | but can be used on the bodies of functions. There are many facilities |
| 463 | including the ability to summarize or get a high-level view of code, |
| 464 | determining dependencies between variables, code improvement suggestions.") |
| 465 | ;; Any version of the GPL |
| 466 | (license (list license:gpl2+ license:gpl3+)))) |
| 467 | |
| 468 | (define-public r-chippeakanno |
| 469 | (package |
| 470 | (name "r-chippeakanno") |
| 471 | (version "3.16.1") |
| 472 | (source |
| 473 | (origin |
| 474 | (method url-fetch) |
| 475 | (uri (bioconductor-uri "ChIPpeakAnno" version)) |
| 476 | (sha256 |
| 477 | (base32 |
| 478 | "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3")))) |
| 479 | (properties `((upstream-name . "ChIPpeakAnno"))) |
| 480 | (build-system r-build-system) |
| 481 | (propagated-inputs |
| 482 | `(("r-biocgenerics" ,r-biocgenerics) |
| 483 | ("r-biocmanager" ,r-biocmanager) |
| 484 | ("r-biostrings" ,r-biostrings) |
| 485 | ("r-delayedarray" ,r-delayedarray) |
| 486 | ("r-go-db" ,r-go-db) |
| 487 | ("r-biomart" ,r-biomart) |
| 488 | ("r-bsgenome" ,r-bsgenome) |
| 489 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 490 | ("r-genomicranges" ,r-genomicranges) |
| 491 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 492 | ("r-iranges" ,r-iranges) |
| 493 | ("r-matrixstats" ,r-matrixstats) |
| 494 | ("r-annotationdbi" ,r-annotationdbi) |
| 495 | ("r-limma" ,r-limma) |
| 496 | ("r-multtest" ,r-multtest) |
| 497 | ("r-rbgl" ,r-rbgl) |
| 498 | ("r-graph" ,r-graph) |
| 499 | ("r-regioner" ,r-regioner) |
| 500 | ("r-dbi" ,r-dbi) |
| 501 | ("r-ensembldb" ,r-ensembldb) |
| 502 | ("r-biobase" ,r-biobase) |
| 503 | ("r-s4vectors" ,r-s4vectors) |
| 504 | ("r-seqinr" ,r-seqinr) |
| 505 | ("r-idr" ,r-idr) |
| 506 | ("r-genomicalignments" ,r-genomicalignments) |
| 507 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 508 | ("r-rsamtools" ,r-rsamtools) |
| 509 | ("r-venndiagram" ,r-venndiagram))) |
| 510 | (home-page "http://bioconductor.org/packages/ChIPpeakAnno") |
| 511 | (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments") |
| 512 | (description |
| 513 | "The package includes functions to retrieve the sequences around the peak, |
| 514 | obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or |
| 515 | custom features such as most conserved elements and other transcription factor |
| 516 | binding sites supplied by users. Starting 2.0.5, new functions have been added |
| 517 | for finding the peaks with bi-directional promoters with summary statistics |
| 518 | (peaksNearBDP), for summarizing the occurrence of motifs in peaks |
| 519 | (summarizePatternInPeaks) and for adding other IDs to annotated peaks or |
| 520 | enrichedGO (addGeneIDs).") |
| 521 | (license license:gpl2+))) |
| 522 | |
| 523 | (define-public r-marray |
| 524 | (package |
| 525 | (name "r-marray") |
| 526 | (version "1.60.0") |
| 527 | (source (origin |
| 528 | (method url-fetch) |
| 529 | (uri (bioconductor-uri "marray" version)) |
| 530 | (sha256 |
| 531 | (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky")))) |
| 532 | (build-system r-build-system) |
| 533 | (propagated-inputs |
| 534 | `(("r-limma" ,r-limma))) |
| 535 | (home-page "http://bioconductor.org/packages/marray") |
| 536 | (synopsis "Exploratory analysis for two-color spotted microarray data") |
| 537 | (description "This package contains class definitions for two-color spotted |
| 538 | microarray data. It also includes fuctions for data input, diagnostic plots, |
| 539 | normalization and quality checking.") |
| 540 | (license license:lgpl2.0+))) |
| 541 | |
| 542 | (define-public r-cghbase |
| 543 | (package |
| 544 | (name "r-cghbase") |
| 545 | (version "1.42.0") |
| 546 | (source (origin |
| 547 | (method url-fetch) |
| 548 | (uri (bioconductor-uri "CGHbase" version)) |
| 549 | (sha256 |
| 550 | (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc")))) |
| 551 | (properties `((upstream-name . "CGHbase"))) |
| 552 | (build-system r-build-system) |
| 553 | (propagated-inputs |
| 554 | `(("r-biobase" ,r-biobase) |
| 555 | ("r-marray" ,r-marray))) |
| 556 | (home-page "http://bioconductor.org/packages/CGHbase") |
| 557 | (synopsis "Base functions and classes for arrayCGH data analysis") |
| 558 | (description "This package contains functions and classes that are needed by |
| 559 | the @code{arrayCGH} packages.") |
| 560 | (license license:gpl2+))) |
| 561 | |
| 562 | (define-public r-cghcall |
| 563 | (package |
| 564 | (name "r-cghcall") |
| 565 | (version "2.44.0") |
| 566 | (source (origin |
| 567 | (method url-fetch) |
| 568 | (uri (bioconductor-uri "CGHcall" version)) |
| 569 | (sha256 |
| 570 | (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi")))) |
| 571 | (properties `((upstream-name . "CGHcall"))) |
| 572 | (build-system r-build-system) |
| 573 | (propagated-inputs |
| 574 | `(("r-biobase" ,r-biobase) |
| 575 | ("r-cghbase" ,r-cghbase) |
| 576 | ("r-impute" ,r-impute) |
| 577 | ("r-dnacopy" ,r-dnacopy) |
| 578 | ("r-snowfall" ,r-snowfall))) |
| 579 | (home-page "http://bioconductor.org/packages/CGHcall") |
| 580 | (synopsis "Base functions and classes for arrayCGH data analysis") |
| 581 | (description "This package contains functions and classes that are needed by |
| 582 | @code{arrayCGH} packages.") |
| 583 | (license license:gpl2+))) |
| 584 | |
| 585 | (define-public r-qdnaseq |
| 586 | (package |
| 587 | (name "r-qdnaseq") |
| 588 | (version "1.18.0") |
| 589 | (source (origin |
| 590 | (method url-fetch) |
| 591 | (uri (bioconductor-uri "QDNAseq" version)) |
| 592 | (sha256 |
| 593 | (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2")))) |
| 594 | (properties `((upstream-name . "QDNAseq"))) |
| 595 | (build-system r-build-system) |
| 596 | (propagated-inputs |
| 597 | `(("r-biobase" ,r-biobase) |
| 598 | ("r-biocparallel" ,r-biocparallel) |
| 599 | ("r-cghbase" ,r-cghbase) |
| 600 | ("r-cghcall" ,r-cghcall) |
| 601 | ("r-dnacopy" ,r-dnacopy) |
| 602 | ("r-genomicranges" ,r-genomicranges) |
| 603 | ("r-iranges" ,r-iranges) |
| 604 | ("r-matrixstats" ,r-matrixstats) |
| 605 | ("r-r-utils" ,r-r-utils) |
| 606 | ("r-rsamtools" ,r-rsamtools))) |
| 607 | (home-page "http://bioconductor.org/packages/QDNAseq") |
| 608 | (synopsis "Quantitative DNA sequencing for chromosomal aberrations") |
| 609 | (description "The genome is divided into non-overlapping fixed-sized bins, |
| 610 | number of sequence reads in each counted, adjusted with a simultaneous |
| 611 | two-dimensional loess correction for sequence mappability and GC content, and |
| 612 | filtered to remove spurious regions in the genome. Downstream steps of |
| 613 | segmentation and calling are also implemented via packages DNAcopy and CGHcall, |
| 614 | respectively.") |
| 615 | (license license:gpl2+))) |
| 616 | |
| 617 | (define-public r-bayseq |
| 618 | (package |
| 619 | (name "r-bayseq") |
| 620 | (version "2.16.0") |
| 621 | (source |
| 622 | (origin |
| 623 | (method url-fetch) |
| 624 | (uri (bioconductor-uri "baySeq" version)) |
| 625 | (sha256 |
| 626 | (base32 |
| 627 | "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5")))) |
| 628 | (properties `((upstream-name . "baySeq"))) |
| 629 | (build-system r-build-system) |
| 630 | (propagated-inputs |
| 631 | `(("r-abind" ,r-abind) |
| 632 | ("r-edger" ,r-edger) |
| 633 | ("r-genomicranges" ,r-genomicranges))) |
| 634 | (home-page "https://bioconductor.org/packages/baySeq/") |
| 635 | (synopsis "Bayesian analysis of differential expression patterns in count data") |
| 636 | (description |
| 637 | "This package identifies differential expression in high-throughput count |
| 638 | data, such as that derived from next-generation sequencing machines, |
| 639 | calculating estimated posterior likelihoods of differential expression (or |
| 640 | more complex hypotheses) via empirical Bayesian methods.") |
| 641 | (license license:gpl3))) |
| 642 | |
| 643 | (define-public r-chipcomp |
| 644 | (package |
| 645 | (name "r-chipcomp") |
| 646 | (version "1.12.0") |
| 647 | (source |
| 648 | (origin |
| 649 | (method url-fetch) |
| 650 | (uri (bioconductor-uri "ChIPComp" version)) |
| 651 | (sha256 |
| 652 | (base32 |
| 653 | "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85")))) |
| 654 | (properties `((upstream-name . "ChIPComp"))) |
| 655 | (build-system r-build-system) |
| 656 | (propagated-inputs |
| 657 | `(("r-biocgenerics" ,r-biocgenerics) |
| 658 | ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19) |
| 659 | ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9) |
| 660 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 661 | ("r-genomicranges" ,r-genomicranges) |
| 662 | ("r-iranges" ,r-iranges) |
| 663 | ("r-limma" ,r-limma) |
| 664 | ("r-rsamtools" ,r-rsamtools) |
| 665 | ("r-rtracklayer" ,r-rtracklayer) |
| 666 | ("r-s4vectors" ,r-s4vectors))) |
| 667 | (home-page "https://bioconductor.org/packages/ChIPComp") |
| 668 | (synopsis "Quantitative comparison of multiple ChIP-seq datasets") |
| 669 | (description |
| 670 | "ChIPComp implements a statistical method for quantitative comparison of |
| 671 | multiple ChIP-seq datasets. It detects differentially bound sharp binding |
| 672 | sites across multiple conditions considering matching control in ChIP-seq |
| 673 | datasets.") |
| 674 | ;; Any version of the GPL. |
| 675 | (license license:gpl3+))) |
| 676 | |
| 677 | (define-public r-riboprofiling |
| 678 | (package |
| 679 | (name "r-riboprofiling") |
| 680 | (version "1.12.0") |
| 681 | (source |
| 682 | (origin |
| 683 | (method url-fetch) |
| 684 | (uri (bioconductor-uri "RiboProfiling" version)) |
| 685 | (sha256 |
| 686 | (base32 |
| 687 | "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z")))) |
| 688 | (properties `((upstream-name . "RiboProfiling"))) |
| 689 | (build-system r-build-system) |
| 690 | (propagated-inputs |
| 691 | `(("r-biocgenerics" ,r-biocgenerics) |
| 692 | ("r-biostrings" ,r-biostrings) |
| 693 | ("r-data-table" ,r-data-table) |
| 694 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 695 | ("r-genomicalignments" ,r-genomicalignments) |
| 696 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 697 | ("r-genomicranges" ,r-genomicranges) |
| 698 | ("r-ggbio" ,r-ggbio) |
| 699 | ("r-ggplot2" ,r-ggplot2) |
| 700 | ("r-iranges" ,r-iranges) |
| 701 | ("r-plyr" ,r-plyr) |
| 702 | ("r-reshape2" ,r-reshape2) |
| 703 | ("r-rsamtools" ,r-rsamtools) |
| 704 | ("r-rtracklayer" ,r-rtracklayer) |
| 705 | ("r-s4vectors" ,r-s4vectors) |
| 706 | ("r-sqldf" ,r-sqldf))) |
| 707 | (home-page "https://bioconductor.org/packages/RiboProfiling/") |
| 708 | (synopsis "Ribosome profiling data analysis") |
| 709 | (description "Starting with a BAM file, this package provides the |
| 710 | necessary functions for quality assessment, read start position recalibration, |
| 711 | the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting |
| 712 | of count data: pairs, log fold-change, codon frequency and coverage |
| 713 | assessment, principal component analysis on codon coverage.") |
| 714 | (license license:gpl3))) |
| 715 | |
| 716 | (define-public r-riboseqr |
| 717 | (package |
| 718 | (name "r-riboseqr") |
| 719 | (version "1.16.0") |
| 720 | (source |
| 721 | (origin |
| 722 | (method url-fetch) |
| 723 | (uri (bioconductor-uri "riboSeqR" version)) |
| 724 | (sha256 |
| 725 | (base32 |
| 726 | "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb")))) |
| 727 | (properties `((upstream-name . "riboSeqR"))) |
| 728 | (build-system r-build-system) |
| 729 | (propagated-inputs |
| 730 | `(("r-abind" ,r-abind) |
| 731 | ("r-bayseq" ,r-bayseq) |
| 732 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 733 | ("r-genomicranges" ,r-genomicranges) |
| 734 | ("r-iranges" ,r-iranges) |
| 735 | ("r-rsamtools" ,r-rsamtools) |
| 736 | ("r-seqlogo" ,r-seqlogo))) |
| 737 | (home-page "https://bioconductor.org/packages/riboSeqR/") |
| 738 | (synopsis "Analysis of sequencing data from ribosome profiling experiments") |
| 739 | (description |
| 740 | "This package provides plotting functions, frameshift detection and |
| 741 | parsing of genetic sequencing data from ribosome profiling experiments.") |
| 742 | (license license:gpl3))) |
| 743 | |
| 744 | (define-public r-interactionset |
| 745 | (package |
| 746 | (name "r-interactionset") |
| 747 | (version "1.10.0") |
| 748 | (source |
| 749 | (origin |
| 750 | (method url-fetch) |
| 751 | (uri (bioconductor-uri "InteractionSet" version)) |
| 752 | (sha256 |
| 753 | (base32 |
| 754 | "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb")))) |
| 755 | (properties |
| 756 | `((upstream-name . "InteractionSet"))) |
| 757 | (build-system r-build-system) |
| 758 | (propagated-inputs |
| 759 | `(("r-biocgenerics" ,r-biocgenerics) |
| 760 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 761 | ("r-genomicranges" ,r-genomicranges) |
| 762 | ("r-iranges" ,r-iranges) |
| 763 | ("r-matrix" ,r-matrix) |
| 764 | ("r-rcpp" ,r-rcpp) |
| 765 | ("r-s4vectors" ,r-s4vectors) |
| 766 | ("r-summarizedexperiment" ,r-summarizedexperiment))) |
| 767 | (home-page "https://bioconductor.org/packages/InteractionSet") |
| 768 | (synopsis "Base classes for storing genomic interaction data") |
| 769 | (description |
| 770 | "This packages provides the @code{GInteractions}, |
| 771 | @code{InteractionSet} and @code{ContactMatrix} objects and associated methods |
| 772 | for storing and manipulating genomic interaction data from Hi-C and ChIA-PET |
| 773 | experiments.") |
| 774 | (license license:gpl3))) |
| 775 | |
| 776 | (define-public r-genomicinteractions |
| 777 | (package |
| 778 | (name "r-genomicinteractions") |
| 779 | (version "1.16.0") |
| 780 | (source |
| 781 | (origin |
| 782 | (method url-fetch) |
| 783 | (uri (bioconductor-uri "GenomicInteractions" version)) |
| 784 | (sha256 |
| 785 | (base32 |
| 786 | "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q")))) |
| 787 | (properties |
| 788 | `((upstream-name . "GenomicInteractions"))) |
| 789 | (build-system r-build-system) |
| 790 | (propagated-inputs |
| 791 | `(("r-biobase" ,r-biobase) |
| 792 | ("r-biocgenerics" ,r-biocgenerics) |
| 793 | ("r-data-table" ,r-data-table) |
| 794 | ("r-dplyr" ,r-dplyr) |
| 795 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 796 | ("r-genomicranges" ,r-genomicranges) |
| 797 | ("r-ggplot2" ,r-ggplot2) |
| 798 | ("r-gridextra" ,r-gridextra) |
| 799 | ("r-gviz" ,r-gviz) |
| 800 | ("r-igraph" ,r-igraph) |
| 801 | ("r-interactionset" ,r-interactionset) |
| 802 | ("r-iranges" ,r-iranges) |
| 803 | ("r-rsamtools" ,r-rsamtools) |
| 804 | ("r-rtracklayer" ,r-rtracklayer) |
| 805 | ("r-s4vectors" ,r-s4vectors) |
| 806 | ("r-stringr" ,r-stringr))) |
| 807 | (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/") |
| 808 | (synopsis "R package for handling genomic interaction data") |
| 809 | (description |
| 810 | "This R package provides tools for handling genomic interaction data, |
| 811 | such as ChIA-PET/Hi-C, annotating genomic features with interaction |
| 812 | information and producing various plots and statistics.") |
| 813 | (license license:gpl3))) |
| 814 | |
| 815 | (define-public r-ctc |
| 816 | (package |
| 817 | (name "r-ctc") |
| 818 | (version "1.56.0") |
| 819 | (source |
| 820 | (origin |
| 821 | (method url-fetch) |
| 822 | (uri (bioconductor-uri "ctc" version)) |
| 823 | (sha256 |
| 824 | (base32 |
| 825 | "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2")))) |
| 826 | (build-system r-build-system) |
| 827 | (propagated-inputs `(("r-amap" ,r-amap))) |
| 828 | (home-page "https://bioconductor.org/packages/ctc/") |
| 829 | (synopsis "Cluster and tree conversion") |
| 830 | (description |
| 831 | "This package provides tools for exporting and importing classification |
| 832 | trees and clusters to other programs.") |
| 833 | (license license:gpl2))) |
| 834 | |
| 835 | (define-public r-goseq |
| 836 | (package |
| 837 | (name "r-goseq") |
| 838 | (version "1.34.1") |
| 839 | (source |
| 840 | (origin |
| 841 | (method url-fetch) |
| 842 | (uri (bioconductor-uri "goseq" version)) |
| 843 | (sha256 |
| 844 | (base32 |
| 845 | "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn")))) |
| 846 | (build-system r-build-system) |
| 847 | (propagated-inputs |
| 848 | `(("r-annotationdbi" ,r-annotationdbi) |
| 849 | ("r-biasedurn" ,r-biasedurn) |
| 850 | ("r-biocgenerics" ,r-biocgenerics) |
| 851 | ("r-genelendatabase" ,r-genelendatabase) |
| 852 | ("r-go-db" ,r-go-db) |
| 853 | ("r-mgcv" ,r-mgcv))) |
| 854 | (home-page "https://bioconductor.org/packages/goseq/") |
| 855 | (synopsis "Gene Ontology analyser for RNA-seq and other length biased data") |
| 856 | (description |
| 857 | "This package provides tools to detect Gene Ontology and/or other user |
| 858 | defined categories which are over/under represented in RNA-seq data.") |
| 859 | (license license:lgpl2.0+))) |
| 860 | |
| 861 | (define-public r-glimma |
| 862 | (package |
| 863 | (name "r-glimma") |
| 864 | (version "1.10.1") |
| 865 | (source |
| 866 | (origin |
| 867 | (method url-fetch) |
| 868 | (uri (bioconductor-uri "Glimma" version)) |
| 869 | (sha256 |
| 870 | (base32 |
| 871 | "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv")))) |
| 872 | (properties `((upstream-name . "Glimma"))) |
| 873 | (build-system r-build-system) |
| 874 | (propagated-inputs |
| 875 | `(("r-edger" ,r-edger) |
| 876 | ("r-jsonlite" ,r-jsonlite) |
| 877 | ("r-s4vectors" ,r-s4vectors))) |
| 878 | (home-page "https://github.com/Shians/Glimma") |
| 879 | (synopsis "Interactive HTML graphics") |
| 880 | (description |
| 881 | "This package generates interactive visualisations for analysis of |
| 882 | RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an |
| 883 | HTML page. The interactions are built on top of the popular static |
| 884 | representations of analysis results in order to provide additional |
| 885 | information.") |
| 886 | (license license:lgpl3))) |
| 887 | |
| 888 | (define-public r-rots |
| 889 | (package |
| 890 | (name "r-rots") |
| 891 | (version "1.10.1") |
| 892 | (source |
| 893 | (origin |
| 894 | (method url-fetch) |
| 895 | (uri (bioconductor-uri "ROTS" version)) |
| 896 | (sha256 |
| 897 | (base32 |
| 898 | "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6")))) |
| 899 | (properties `((upstream-name . "ROTS"))) |
| 900 | (build-system r-build-system) |
| 901 | (propagated-inputs |
| 902 | `(("r-biobase" ,r-biobase) |
| 903 | ("r-rcpp" ,r-rcpp))) |
| 904 | (home-page "https://bioconductor.org/packages/ROTS/") |
| 905 | (synopsis "Reproducibility-Optimized Test Statistic") |
| 906 | (description |
| 907 | "This package provides tools for calculating the |
| 908 | @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing |
| 909 | in omics data.") |
| 910 | (license license:gpl2+))) |
| 911 | |
| 912 | (define-public r-plgem |
| 913 | (package |
| 914 | (name "r-plgem") |
| 915 | (version "1.54.1") |
| 916 | (source |
| 917 | (origin |
| 918 | (method url-fetch) |
| 919 | (uri (bioconductor-uri "plgem" version)) |
| 920 | (sha256 |
| 921 | (base32 |
| 922 | "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg")))) |
| 923 | (build-system r-build-system) |
| 924 | (propagated-inputs |
| 925 | `(("r-biobase" ,r-biobase) |
| 926 | ("r-mass" ,r-mass))) |
| 927 | (home-page "http://www.genopolis.it") |
| 928 | (synopsis "Detect differential expression in microarray and proteomics datasets") |
| 929 | (description |
| 930 | "The Power Law Global Error Model (PLGEM) has been shown to faithfully |
| 931 | model the variance-versus-mean dependence that exists in a variety of |
| 932 | genome-wide datasets, including microarray and proteomics data. The use of |
| 933 | PLGEM has been shown to improve the detection of differentially expressed |
| 934 | genes or proteins in these datasets.") |
| 935 | (license license:gpl2))) |
| 936 | |
| 937 | (define-public r-inspect |
| 938 | (package |
| 939 | (name "r-inspect") |
| 940 | (version "1.12.1") |
| 941 | (source |
| 942 | (origin |
| 943 | (method url-fetch) |
| 944 | (uri (bioconductor-uri "INSPEcT" version)) |
| 945 | (sha256 |
| 946 | (base32 |
| 947 | "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp")))) |
| 948 | (properties `((upstream-name . "INSPEcT"))) |
| 949 | (build-system r-build-system) |
| 950 | (propagated-inputs |
| 951 | `(("r-biobase" ,r-biobase) |
| 952 | ("r-biocgenerics" ,r-biocgenerics) |
| 953 | ("r-biocparallel" ,r-biocparallel) |
| 954 | ("r-deseq2" ,r-deseq2) |
| 955 | ("r-desolve" ,r-desolve) |
| 956 | ("r-genomicalignments" ,r-genomicalignments) |
| 957 | ("r-genomicfeatures" ,r-genomicfeatures) |
| 958 | ("r-genomicranges" ,r-genomicranges) |
| 959 | ("r-iranges" ,r-iranges) |
| 960 | ("r-plgem" ,r-plgem) |
| 961 | ("r-preprocesscore" ,r-preprocesscore) |
| 962 | ("r-proc" ,r-proc) |
| 963 | ("r-rootsolve" ,r-rootsolve) |
| 964 | ("r-rsamtools" ,r-rsamtools) |
| 965 | ("r-s4vectors" ,r-s4vectors) |
| 966 | ("r-shiny" ,r-shiny) |
| 967 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 968 | ("r-txdb-mmusculus-ucsc-mm9-knowngene" |
| 969 | ,r-txdb-mmusculus-ucsc-mm9-knowngene))) |
| 970 | (home-page "https://bioconductor.org/packages/INSPEcT") |
| 971 | (synopsis "Analysis of 4sU-seq and RNA-seq time-course data") |
| 972 | (description |
| 973 | "INSPEcT (INference of Synthesis, Processing and dEgradation rates in |
| 974 | Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in |
| 975 | order to evaluate synthesis, processing and degradation rates and assess via |
| 976 | modeling the rates that determines changes in mature mRNA levels.") |
| 977 | (license license:gpl2))) |
| 978 | |
| 979 | (define-public r-dnabarcodes |
| 980 | (package |
| 981 | (name "r-dnabarcodes") |
| 982 | (version "1.12.0") |
| 983 | (source |
| 984 | (origin |
| 985 | (method url-fetch) |
| 986 | (uri (bioconductor-uri "DNABarcodes" version)) |
| 987 | (sha256 |
| 988 | (base32 |
| 989 | "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0")))) |
| 990 | (properties `((upstream-name . "DNABarcodes"))) |
| 991 | (build-system r-build-system) |
| 992 | (propagated-inputs |
| 993 | `(("r-bh" ,r-bh) |
| 994 | ("r-matrix" ,r-matrix) |
| 995 | ("r-rcpp" ,r-rcpp))) |
| 996 | (home-page "https://bioconductor.org/packages/DNABarcodes") |
| 997 | (synopsis "Create and analyze DNA barcodes") |
| 998 | (description |
| 999 | "This package offers tools to create DNA barcode sets capable of |
| 1000 | correcting insertion, deletion, and substitution errors. Existing barcodes |
| 1001 | can be analyzed regarding their minimal, maximal and average distances between |
| 1002 | barcodes. Finally, reads that start with a (possibly mutated) barcode can be |
| 1003 | demultiplexed, i.e. assigned to their original reference barcode.") |
| 1004 | (license license:gpl2))) |
| 1005 | |
| 1006 | (define-public r-ruvseq |
| 1007 | (package |
| 1008 | (name "r-ruvseq") |
| 1009 | (version "1.16.1") |
| 1010 | (source |
| 1011 | (origin |
| 1012 | (method url-fetch) |
| 1013 | (uri (bioconductor-uri "RUVSeq" version)) |
| 1014 | (sha256 |
| 1015 | (base32 |
| 1016 | "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv")))) |
| 1017 | (properties `((upstream-name . "RUVSeq"))) |
| 1018 | (build-system r-build-system) |
| 1019 | (propagated-inputs |
| 1020 | `(("r-biobase" ,r-biobase) |
| 1021 | ("r-edaseq" ,r-edaseq) |
| 1022 | ("r-edger" ,r-edger) |
| 1023 | ("r-mass" ,r-mass))) |
| 1024 | (home-page "https://github.com/drisso/RUVSeq") |
| 1025 | (synopsis "Remove unwanted variation from RNA-Seq data") |
| 1026 | (description |
| 1027 | "This package implements methods to @dfn{remove unwanted variation} (RUV) |
| 1028 | of Risso et al. (2014) for the normalization of RNA-Seq read counts between |
| 1029 | samples.") |
| 1030 | (license license:artistic2.0))) |
| 1031 | |
| 1032 | (define-public r-biocneighbors |
| 1033 | (package |
| 1034 | (name "r-biocneighbors") |
| 1035 | (version "1.0.0") |
| 1036 | (source |
| 1037 | (origin |
| 1038 | (method url-fetch) |
| 1039 | (uri (bioconductor-uri "BiocNeighbors" version)) |
| 1040 | (sha256 |
| 1041 | (base32 |
| 1042 | "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll")))) |
| 1043 | (properties `((upstream-name . "BiocNeighbors"))) |
| 1044 | (build-system r-build-system) |
| 1045 | (propagated-inputs |
| 1046 | `(("r-biocparallel" ,r-biocparallel) |
| 1047 | ("r-rcpp" ,r-rcpp) |
| 1048 | ("r-rcppannoy" ,r-rcppannoy) |
| 1049 | ("r-s4vectors" ,r-s4vectors))) |
| 1050 | (home-page "https://bioconductor.org/packages/BiocNeighbors") |
| 1051 | (synopsis "Nearest Neighbor Detection for Bioconductor packages") |
| 1052 | (description |
| 1053 | "This package implements exact and approximate methods for nearest |
| 1054 | neighbor detection, in a framework that allows them to be easily switched |
| 1055 | within Bioconductor packages or workflows. The exact algorithm is implemented |
| 1056 | using pre-clustering with the k-means algorithm. Functions are also provided |
| 1057 | to search for all neighbors within a given distance. Parallelization is |
| 1058 | achieved for all methods using the BiocParallel framework.") |
| 1059 | (license license:gpl3))) |
| 1060 | |
| 1061 | (define-public r-destiny |
| 1062 | (package |
| 1063 | (name "r-destiny") |
| 1064 | (version "2.12.0") |
| 1065 | (source |
| 1066 | (origin |
| 1067 | (method url-fetch) |
| 1068 | (uri (bioconductor-uri "destiny" version)) |
| 1069 | (sha256 |
| 1070 | (base32 |
| 1071 | "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67")))) |
| 1072 | (build-system r-build-system) |
| 1073 | (propagated-inputs |
| 1074 | `(("r-biobase" ,r-biobase) |
| 1075 | ("r-biocgenerics" ,r-biocgenerics) |
| 1076 | ("r-fnn" ,r-fnn) |
| 1077 | ("r-ggthemes" ,r-ggthemes) |
| 1078 | ("r-hmisc" ,r-hmisc) |
| 1079 | ("r-igraph" ,r-igraph) |
| 1080 | ("r-matrix" ,r-matrix) |
| 1081 | ("r-proxy" ,r-proxy) |
| 1082 | ("r-rcpp" ,r-rcpp) |
| 1083 | ("r-rcppeigen" ,r-rcppeigen) |
| 1084 | ("r-scales" ,r-scales) |
| 1085 | ("r-scatterplot3d" ,r-scatterplot3d) |
| 1086 | ("r-smoother" ,r-smoother) |
| 1087 | ("r-summarizedexperiment" ,r-summarizedexperiment) |
| 1088 | ("r-vim" ,r-vim))) |
| 1089 | (home-page "https://bioconductor.org/packages/destiny/") |
| 1090 | (synopsis "Create and plot diffusion maps") |
| 1091 | (description "This package provides tools to create and plot diffusion |
| 1092 | maps.") |
| 1093 | ;; Any version of the GPL |
| 1094 | (license license:gpl3+))) |
| 1095 | |
| 1096 | (define-public r-savr |
| 1097 | (package |
| 1098 | (name "r-savr") |
| 1099 | (version "1.20.0") |
| 1100 | (source |
| 1101 | (origin |
| 1102 | (method url-fetch) |
| 1103 | (uri (bioconductor-uri "savR" version)) |
| 1104 | (sha256 |
| 1105 | (base32 |
| 1106 | "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7")))) |
| 1107 | (properties `((upstream-name . "savR"))) |
| 1108 | (build-system r-build-system) |
| 1109 | (propagated-inputs |
| 1110 | `(("r-ggplot2" ,r-ggplot2) |
| 1111 | ("r-gridextra" ,r-gridextra) |
| 1112 | ("r-reshape2" ,r-reshape2) |
| 1113 | ("r-scales" ,r-scales) |
| 1114 | ("r-xml" ,r-xml))) |
| 1115 | (home-page "https://github.com/bcalder/savR") |
| 1116 | (synopsis "Parse and analyze Illumina SAV files") |
| 1117 | (description |
| 1118 | "This package provides tools to parse Illumina Sequence Analysis |
| 1119 | Viewer (SAV) files, access data, and generate QC plots.") |
| 1120 | (license license:agpl3+))) |
| 1121 | |
| 1122 | (define-public r-chipexoqual |
| 1123 | (package |
| 1124 | (name "r-chipexoqual") |
| 1125 | (version "1.6.0") |
| 1126 | (source |
| 1127 | (origin |
| 1128 | (method url-fetch) |
| 1129 | (uri (bioconductor-uri "ChIPexoQual" version)) |
| 1130 | (sha256 |
| 1131 | (base32 |
| 1132 | "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp")))) |
| 1133 | (properties `((upstream-name . "ChIPexoQual"))) |
| 1134 | (build-system r-build-system) |
| 1135 | (propagated-inputs |
| 1136 | `(("r-biocparallel" ,r-biocparallel) |
| 1137 | ("r-biovizbase" ,r-biovizbase) |
| 1138 | ("r-broom" ,r-broom) |
| 1139 | ("r-data-table" ,r-data-table) |
| 1140 | ("r-dplyr" ,r-dplyr) |
| 1141 | ("r-genomeinfodb" ,r-genomeinfodb) |
| 1142 | ("r-genomicalignments" ,r-genomicalignments) |
| 1143 | ("r-genomicranges" ,r-genomicranges) |
| 1144 | ("r-ggplot2" ,r-ggplot2) |
| 1145 | ("r-hexbin" ,r-hexbin) |
| 1146 | ("r-iranges" ,r-iranges) |
| 1147 | ("r-rcolorbrewer" ,r-rcolorbrewer) |
| 1148 | ("r-rmarkdown" ,r-rmarkdown) |
| 1149 | ("r-rsamtools" ,r-rsamtools) |
| 1150 | ("r-s4vectors" ,r-s4vectors) |
| 1151 | ("r-scales" ,r-scales) |
| 1152 | ("r-viridis" ,r-viridis))) |
| 1153 | (home-page "https://github.com/keleslab/ChIPexoQual") |
| 1154 | (synopsis "Quality control pipeline for ChIP-exo/nexus data") |
| 1155 | (description |
| 1156 | "This package provides a quality control pipeline for ChIP-exo/nexus |
| 1157 | sequencing data.") |
| 1158 | (license license:gpl2+))) |