gnu/packages/bioconductor.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 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 statistics))
  32
  33 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
  34   (package
  35     (name "r-bsgenome-dmelanogaster-ucsc-dm6")
  36     (version "1.4.1")
  37     (source (origin
  38               (method url-fetch)
  39               ;; We cannot use bioconductor-uri here because this tarball is
  40               ;; located under "data/annotation/" instead of "bioc/".
  41               (uri (string-append "https://www.bioconductor.org/packages/"
  42                                   "release/data/annotation/src/contrib/"
  43                                   "BSgenome.Dmelanogaster.UCSC.dm6_"
  44                                   version ".tar.gz"))
  45               (sha256
  46                (base32
  47                 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
  48     (properties
  49      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
  50     (build-system r-build-system)
  51     ;; As this package provides little more than a very large data file it
  52     ;; doesn't make sense to build substitutes.
  53     (arguments `(#:substitutable? #f))
  54     (propagated-inputs
  55      `(("r-bsgenome" ,r-bsgenome)))
  56     (home-page
  57      "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
  58     (synopsis "Full genome sequences for Fly")
  59     (description
  60      "This package provides full genome sequences for Drosophila
  61 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
  62 objects.")
  63     (license license:artistic2.0)))
  64
  65 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
  66   (package
  67     (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
  68     (version "1.3.99")
  69     (source (origin
  70               (method url-fetch)
  71               ;; We cannot use bioconductor-uri here because this tarball is
  72               ;; located under "data/annotation/" instead of "bioc/".
  73               (uri (string-append "http://www.bioconductor.org/packages/"
  74                                   "release/data/annotation/src/contrib/"
  75                                   "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
  76                                   version ".tar.gz"))
  77               (sha256
  78                (base32
  79                 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
  80     (properties
  81      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
  82     (build-system r-build-system)
  83     (propagated-inputs
  84      `(("r-bsgenome" ,r-bsgenome)
  85        ("r-bsgenome-dmelanogaster-ucsc-dm3"
  86         ,r-bsgenome-dmelanogaster-ucsc-dm3)))
  87     (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
  88     (synopsis "Full masked genome sequences for Fly")
  89     (description
  90      "This package provides full masked genome sequences for Drosophila
  91 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
  92 Biostrings objects.  The sequences are the same as in
  93 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
  94 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
  95 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
  96 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
  97 Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
  98     (license license:artistic2.0)))
  99
 100 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
 101   (package
 102     (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
 103     (version "1.3.99")
 104     (source (origin
 105               (method url-fetch)
 106               ;; We cannot use bioconductor-uri here because this tarball is
 107               ;; located under "data/annotation/" instead of "bioc/".
 108               (uri (string-append "http://www.bioconductor.org/packages/"
 109                                   "release/data/annotation/src/contrib/"
 110                                   "BSgenome.Hsapiens.UCSC.hg19.masked_"
 111                                   version ".tar.gz"))
 112               (sha256
 113                (base32
 114                 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
 115     (properties
 116      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
 117     (build-system r-build-system)
 118     (propagated-inputs
 119      `(("r-bsgenome" ,r-bsgenome)
 120        ("r-bsgenome-hsapiens-ucsc-hg19"
 121         ,r-bsgenome-hsapiens-ucsc-hg19)))
 122     (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
 123     (synopsis "Full masked genome sequences for Homo sapiens")
 124     (description
 125      "This package provides full genome sequences for Homo sapiens (Human) as
 126 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.  The
 127 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
 128 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
 129 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
 130 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
 131 Repeats Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by
 132 default.")
 133     (license license:artistic2.0)))
 134
 135 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
 136   (package
 137     (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
 138     (version "1.3.99")
 139     (source (origin
 140               (method url-fetch)
 141               ;; We cannot use bioconductor-uri here because this tarball is
 142               ;; located under "data/annotation/" instead of "bioc/".
 143               (uri (string-append "http://www.bioconductor.org/packages/"
 144                                   "release/data/annotation/src/contrib/"
 145                                   "BSgenome.Mmusculus.UCSC.mm9.masked_"
 146                                   version ".tar.gz"))
 147               (sha256
 148                (base32
 149                 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
 150     (properties
 151      `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
 152     (build-system r-build-system)
 153     (propagated-inputs
 154      `(("r-bsgenome" ,r-bsgenome)
 155        ("r-bsgenome-mmusculus-ucsc-mm9"
 156         ,r-bsgenome-mmusculus-ucsc-mm9)))
 157     (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
 158     (synopsis "Full masked genome sequences for Mouse")
 159     (description
 160      "This package provides full genome sequences for Mus musculus (Mouse) as
 161 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.  The
 162 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
 163 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
 164 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
 165 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
 166 Repeats Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by
 167 default."  )
 168     (license license:artistic2.0)))
 169
 170 (define-public r-hpar
 171   (package
 172     (name "r-hpar")
 173     (version "1.22.2")
 174     (source
 175      (origin
 176        (method url-fetch)
 177        (uri (bioconductor-uri "hpar" version))
 178        (sha256
 179         (base32
 180          "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
 181     (build-system r-build-system)
 182     (home-page "https://bioconductor.org/packages/hpar/")
 183     (synopsis "Human Protein Atlas in R")
 184     (description "This package provides a simple interface to and data from
 185 the Human Protein Atlas project.")
 186     (license license:artistic2.0)))
 187
 188 (define-public r-regioner
 189   (package
 190     (name "r-regioner")
 191     (version "1.12.0")
 192     (source
 193      (origin
 194        (method url-fetch)
 195        (uri (bioconductor-uri "regioneR" version))
 196        (sha256
 197         (base32
 198          "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
 199     (properties `((upstream-name . "regioneR")))
 200     (build-system r-build-system)
 201     (propagated-inputs
 202      `(("r-memoise" ,r-memoise)
 203        ("r-genomicranges" ,r-genomicranges)
 204        ("r-bsgenome" ,r-bsgenome)
 205        ("r-rtracklayer" ,r-rtracklayer)
 206        ("r-genomeinfodb" ,r-genomeinfodb)
 207        ("r-iranges" ,r-iranges)
 208        ("r-s4vectors" ,r-s4vectors)))
 209     (home-page "https://bioconductor.org/packages/regioneR/")
 210     (synopsis "Association analysis of genomic regions")
 211     (description "This package offers a statistical framework based on
 212 customizable permutation tests to assess the association between genomic
 213 region sets and other genomic features.")
 214     (license license:artistic2.0)))
 215
 216 (define-public r-diffbind
 217   (package
 218     (name "r-diffbind")
 219     (version "2.8.0")
 220     (source
 221      (origin
 222        (method url-fetch)
 223        (uri (bioconductor-uri "DiffBind" version))
 224        (sha256
 225         (base32
 226          "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
 227     (properties `((upstream-name . "DiffBind")))
 228     (build-system r-build-system)
 229     (inputs
 230      `(("zlib" ,zlib)))
 231     (propagated-inputs
 232      `(("r-amap" ,r-amap)
 233        ("r-biocparallel" ,r-biocparallel)
 234        ("r-deseq2" ,r-deseq2)
 235        ("r-dplyr" ,r-dplyr)
 236        ("r-edger" ,r-edger)
 237        ("r-genomicalignments" ,r-genomicalignments)
 238        ("r-genomicranges" ,r-genomicranges)
 239        ("r-ggplot2" ,r-ggplot2)
 240        ("r-ggrepel" ,r-ggrepel)
 241        ("r-gplots" ,r-gplots)
 242        ("r-iranges" ,r-iranges)
 243        ("r-lattice" ,r-lattice)
 244        ("r-limma" ,r-limma)
 245        ("r-locfit" ,r-locfit)
 246        ("r-rcolorbrewer" , r-rcolorbrewer)
 247        ("r-rcpp" ,r-rcpp)
 248        ("r-rsamtools" ,r-rsamtools)
 249        ("r-s4vectors" ,r-s4vectors)
 250        ("r-summarizedexperiment" ,r-summarizedexperiment)
 251        ("r-systempiper" ,r-systempiper)
 252        ("r-zlibbioc" ,r-zlibbioc)))
 253     (home-page "http://bioconductor.org/packages/DiffBind")
 254     (synopsis "Differential binding analysis of ChIP-Seq peak data")
 255     (description
 256      "This package computes differentially bound sites from multiple
 257 ChIP-seq experiments using affinity (quantitative) data.  Also enables
 258 occupancy (overlap) analysis and plotting functions.")
 259     (license license:artistic2.0)))
 260
 261 (define-public r-ripseeker
 262   (package
 263     (name "r-ripseeker")
 264     (version "1.20.0")
 265     (source
 266      (origin
 267        (method url-fetch)
 268        (uri (bioconductor-uri "RIPSeeker" version))
 269        (sha256
 270         (base32
 271          "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
 272     (properties `((upstream-name . "RIPSeeker")))
 273     (build-system r-build-system)
 274     (propagated-inputs
 275      `(("r-s4vectors" ,r-s4vectors)
 276        ("r-iranges" ,r-iranges)
 277        ("r-genomicranges" ,r-genomicranges)
 278        ("r-summarizedexperiment" ,r-summarizedexperiment)
 279        ("r-rsamtools" ,r-rsamtools)
 280        ("r-genomicalignments" ,r-genomicalignments)
 281        ("r-rtracklayer" ,r-rtracklayer)))
 282     (home-page "http://bioconductor.org/packages/RIPSeeker")
 283     (synopsis
 284      "Identifying protein-associated transcripts from RIP-seq experiments")
 285     (description
 286      "This package infers and discriminates RIP peaks from RIP-seq alignments
 287 using two-state HMM with negative binomial emission probability.  While
 288 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
 289 a suite of bioinformatics tools integrated within this self-contained software
 290 package comprehensively addressing issues ranging from post-alignments
 291 processing to visualization and annotation.")
 292     (license license:gpl2)))
 293
 294 (define-public r-multtest
 295   (package
 296     (name "r-multtest")
 297     (version "2.36.0")
 298     (source
 299      (origin
 300        (method url-fetch)
 301        (uri (bioconductor-uri "multtest" version))
 302        (sha256
 303         (base32
 304          "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
 305     (build-system r-build-system)
 306     (propagated-inputs
 307      `(("r-survival" ,r-survival)
 308        ("r-biocgenerics" ,r-biocgenerics)
 309        ("r-biobase" ,r-biobase)
 310        ("r-mass" ,r-mass)))
 311     (home-page "http://bioconductor.org/packages/multtest")
 312     (synopsis "Resampling-based multiple hypothesis testing")
 313     (description
 314      "This package can do non-parametric bootstrap and permutation
 315 resampling-based multiple testing procedures (including empirical Bayes
 316 methods) for controlling the family-wise error rate (FWER), generalized
 317 family-wise error rate (gFWER), tail probability of the proportion of
 318 false positives (TPPFP), and false discovery rate (FDR).  Several choices
 319 of bootstrap-based null distribution are implemented (centered, centered
 320 and scaled, quantile-transformed).  Single-step and step-wise methods are
 321 available.  Tests based on a variety of T- and F-statistics (including
 322 T-statistics based on regression parameters from linear and survival models
 323 as well as those based on correlation parameters) are included.  When probing
 324 hypotheses with T-statistics, users may also select a potentially faster null
 325 distribution which is multivariate normal with mean zero and variance
 326 covariance matrix derived from the vector influence function.  Results are
 327 reported in terms of adjusted P-values, confidence regions and test statistic
 328 cutoffs.  The procedures are directly applicable to identifying differentially
 329 expressed genes in DNA microarray experiments.")
 330     (license license:lgpl3)))
 331
 332 (define-public r-chippeakanno
 333   (package
 334     (name "r-chippeakanno")
 335     (version "3.14.0")
 336     (source
 337      (origin
 338        (method url-fetch)
 339        (uri (bioconductor-uri "ChIPpeakAnno" version))
 340        (sha256
 341         (base32
 342          "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0"))))
 343     (properties `((upstream-name . "ChIPpeakAnno")))
 344     (build-system r-build-system)
 345     (propagated-inputs
 346      `(("r-biocgenerics" ,r-biocgenerics)
 347        ("r-biostrings" ,r-biostrings)
 348        ("r-delayedarray" ,r-delayedarray)
 349        ("r-go-db" ,r-go-db)
 350        ("r-biomart" ,r-biomart)
 351        ("r-bsgenome" ,r-bsgenome)
 352        ("r-genomicfeatures" ,r-genomicfeatures)
 353        ("r-genomicranges" ,r-genomicranges)
 354        ("r-genomeinfodb" ,r-genomeinfodb)
 355        ("r-iranges" ,r-iranges)
 356        ("r-matrixstats" ,r-matrixstats)
 357        ("r-annotationdbi" ,r-annotationdbi)
 358        ("r-limma" ,r-limma)
 359        ("r-multtest" ,r-multtest)
 360        ("r-rbgl" ,r-rbgl)
 361        ("r-graph" ,r-graph)
 362        ("r-biocinstaller" ,r-biocinstaller)
 363        ("r-regioner" ,r-regioner)
 364        ("r-dbi" ,r-dbi)
 365        ("r-ensembldb" ,r-ensembldb)
 366        ("r-biobase" ,r-biobase)
 367        ("r-s4vectors" ,r-s4vectors)
 368        ("r-seqinr" ,r-seqinr)
 369        ("r-idr" ,r-idr)
 370        ("r-genomicalignments" ,r-genomicalignments)
 371        ("r-summarizedexperiment" ,r-summarizedexperiment)
 372        ("r-rsamtools" ,r-rsamtools)
 373        ("r-venndiagram" ,r-venndiagram)))
 374     (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
 375     (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
 376     (description
 377      "The package includes functions to retrieve the sequences around the peak,
 378 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
 379 custom features such as most conserved elements and other transcription factor
 380 binding sites supplied by users.  Starting 2.0.5, new functions have been added
 381 for finding the peaks with bi-directional promoters with summary statistics
 382 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
 383 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
 384 enrichedGO (addGeneIDs).")
 385     (license license:gpl2+)))
 386
 387 (define-public r-marray
 388   (package
 389     (name "r-marray")
 390     (version "1.58.0")
 391     (source (origin
 392               (method url-fetch)
 393               (uri (bioconductor-uri "marray" version))
 394               (sha256
 395                (base32 "0539flh3y1qy5b1bamkfwbskis765c5s33v1y9j51n33mxb9h08d"))))
 396     (build-system r-build-system)
 397     (propagated-inputs
 398      `(("r-limma" ,r-limma)))
 399     (home-page "http://bioconductor.org/packages/marray")
 400     (synopsis "Exploratory analysis for two-color spotted microarray data")
 401     (description "This package contains class definitions for two-color spotted
 402 microarray data.  It also includes fuctions for data input, diagnostic plots,
 403 normalization and quality checking.")
 404     (license license:lgpl2.0+)))
 405
 406 (define-public r-cghbase
 407   (package
 408    (name "r-cghbase")
 409    (version "1.40.0")
 410    (source (origin
 411             (method url-fetch)
 412             (uri (bioconductor-uri "CGHbase" version))
 413             (sha256
 414              (base32 "1hf44vma3kgwr61kjbszvfxkava8bjqnam1mdncqvczbypb2xwaq"))))
 415    (properties `((upstream-name . "CGHbase")))
 416    (build-system r-build-system)
 417    (propagated-inputs
 418     `(("r-biobase" ,r-biobase)
 419       ("r-marray" ,r-marray)))
 420    (home-page "http://bioconductor.org/packages/CGHbase")
 421    (synopsis "Base functions and classes for arrayCGH data analysis")
 422    (description "This package contains functions and classes that are needed by
 423 the @code{arrayCGH} packages.")
 424    (license license:gpl2+)))
 425
 426 (define-public r-cghcall
 427   (package
 428    (name "r-cghcall")
 429    (version "2.42.0")
 430    (source (origin
 431             (method url-fetch)
 432             (uri (bioconductor-uri "CGHcall" version))
 433             (sha256
 434              (base32 "0y71vfxv9x0am3xvv520yr95cb7m7y92dhdx1vkqki80jrmf12dz"))))
 435    (properties `((upstream-name . "CGHcall")))
 436    (build-system r-build-system)
 437    (propagated-inputs
 438     `(("r-biobase" ,r-biobase)
 439       ("r-cghbase" ,r-cghbase)
 440       ("r-impute" ,r-impute)
 441       ("r-dnacopy" ,r-dnacopy)
 442       ("r-snowfall" ,r-snowfall)))
 443    (home-page "http://bioconductor.org/packages/CGHcall")
 444    (synopsis "Base functions and classes for arrayCGH data analysis")
 445    (description "This package contains functions and classes that are needed by
 446 @code{arrayCGH} packages.")
 447    (license license:gpl2+)))
 448
 449 (define-public r-qdnaseq
 450   (package
 451     (name "r-qdnaseq")
 452     (version "1.16.0")
 453     (source (origin
 454               (method url-fetch)
 455               (uri (bioconductor-uri "QDNAseq" version))
 456               (sha256
 457                (base32 "1pj69mfyxwfd0d7h4kls9xq96sdc55y3rv20qpla50hw9libcwwd"))))
 458     (properties `((upstream-name . "QDNAseq")))
 459     (build-system r-build-system)
 460     (propagated-inputs
 461      `(("r-biobase" ,r-biobase)
 462        ("r-biocparallel" ,r-biocparallel)
 463        ("r-cghbase" ,r-cghbase)
 464        ("r-cghcall" ,r-cghcall)
 465        ("r-dnacopy" ,r-dnacopy)
 466        ("r-genomicranges" ,r-genomicranges)
 467        ("r-iranges" ,r-iranges)
 468        ("r-matrixstats" ,r-matrixstats)
 469        ("r-r-utils" ,r-r-utils)
 470        ("r-rsamtools" ,r-rsamtools)))
 471     (home-page "http://bioconductor.org/packages/QDNAseq")
 472     (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
 473     (description "The genome is divided into non-overlapping fixed-sized bins,
 474 number of sequence reads in each counted, adjusted with a simultaneous
 475 two-dimensional loess correction for sequence mappability and GC content, and
 476 filtered to remove spurious regions in the genome.  Downstream steps of
 477 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
 478 respectively.")
 479     (license license:gpl2+)))
 480
 481 (define-public r-bayseq
 482   (package
 483     (name "r-bayseq")
 484     (version "2.14.0")
 485     (source
 486      (origin
 487        (method url-fetch)
 488        (uri (bioconductor-uri "baySeq" version))
 489        (sha256
 490         (base32
 491          "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
 492     (properties `((upstream-name . "baySeq")))
 493     (build-system r-build-system)
 494     (propagated-inputs
 495      `(("r-abind" ,r-abind)
 496        ("r-edger" ,r-edger)
 497        ("r-genomicranges" ,r-genomicranges)))
 498     (home-page "https://bioconductor.org/packages/baySeq/")
 499     (synopsis "Bayesian analysis of differential expression patterns in count data")
 500     (description
 501      "This package identifies differential expression in high-throughput count
 502 data, such as that derived from next-generation sequencing machines,
 503 calculating estimated posterior likelihoods of differential expression (or
 504 more complex hypotheses) via empirical Bayesian methods.")
 505     (license license:gpl3)))
 506
 507 (define-public r-chipcomp
 508   (package
 509     (name "r-chipcomp")
 510     (version "1.10.0")
 511     (source
 512      (origin
 513        (method url-fetch)
 514        (uri (bioconductor-uri "ChIPComp" version))
 515        (sha256
 516         (base32
 517          "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
 518     (properties `((upstream-name . "ChIPComp")))
 519     (build-system r-build-system)
 520     (propagated-inputs
 521      `(("r-biocgenerics" ,r-biocgenerics)
 522        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
 523        ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
 524        ("r-genomeinfodb" ,r-genomeinfodb)
 525        ("r-genomicranges" ,r-genomicranges)
 526        ("r-iranges" ,r-iranges)
 527        ("r-limma" ,r-limma)
 528        ("r-rsamtools" ,r-rsamtools)
 529        ("r-rtracklayer" ,r-rtracklayer)
 530        ("r-s4vectors" ,r-s4vectors)))
 531     (home-page "https://bioconductor.org/packages/ChIPComp")
 532     (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
 533     (description
 534      "ChIPComp implements a statistical method for quantitative comparison of
 535 multiple ChIP-seq datasets.  It detects differentially bound sharp binding
 536 sites across multiple conditions considering matching control in ChIP-seq
 537 datasets.")
 538     ;; Any version of the GPL.
 539     (license license:gpl3+)))
 540
 541 (define-public r-riboprofiling
 542   (package
 543     (name "r-riboprofiling")
 544     (version "1.10.0")
 545     (source
 546      (origin
 547        (method url-fetch)
 548        (uri (bioconductor-uri "RiboProfiling" version))
 549        (sha256
 550         (base32
 551          "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
 552     (properties `((upstream-name . "RiboProfiling")))
 553     (build-system r-build-system)
 554     (propagated-inputs
 555      `(("r-biocgenerics" ,r-biocgenerics)
 556        ("r-biostrings" ,r-biostrings)
 557        ("r-data-table" ,r-data-table)
 558        ("r-genomeinfodb" ,r-genomeinfodb)
 559        ("r-genomicalignments" ,r-genomicalignments)
 560        ("r-genomicfeatures" ,r-genomicfeatures)
 561        ("r-genomicranges" ,r-genomicranges)
 562        ("r-ggbio" ,r-ggbio)
 563        ("r-ggplot2" ,r-ggplot2)
 564        ("r-iranges" ,r-iranges)
 565        ("r-plyr" ,r-plyr)
 566        ("r-reshape2" ,r-reshape2)
 567        ("r-rsamtools" ,r-rsamtools)
 568        ("r-rtracklayer" ,r-rtracklayer)
 569        ("r-s4vectors" ,r-s4vectors)
 570        ("r-sqldf" ,r-sqldf)))
 571     (home-page "https://bioconductor.org/packages/RiboProfiling/")
 572     (synopsis "Ribosome profiling data analysis")
 573     (description "Starting with a BAM file, this package provides the
 574 necessary functions for quality assessment, read start position recalibration,
 575 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
 576 of count data: pairs, log fold-change, codon frequency and coverage
 577 assessment, principal component analysis on codon coverage.")
 578     (license license:gpl3)))
 579
 580 (define-public r-riboseqr
 581   (package
 582     (name "r-riboseqr")
 583     (version "1.14.0")
 584     (source
 585      (origin
 586        (method url-fetch)
 587        (uri (bioconductor-uri "riboSeqR" version))
 588        (sha256
 589         (base32
 590          "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
 591     (properties `((upstream-name . "riboSeqR")))
 592     (build-system r-build-system)
 593     (propagated-inputs
 594      `(("r-abind" ,r-abind)
 595        ("r-bayseq" ,r-bayseq)
 596        ("r-genomeinfodb" ,r-genomeinfodb)
 597        ("r-genomicranges" ,r-genomicranges)
 598        ("r-iranges" ,r-iranges)
 599        ("r-rsamtools" ,r-rsamtools)
 600        ("r-seqlogo" ,r-seqlogo)))
 601     (home-page "https://bioconductor.org/packages/riboSeqR/")
 602     (synopsis "Analysis of sequencing data from ribosome profiling experiments")
 603     (description
 604      "This package provides plotting functions, frameshift detection and
 605 parsing of genetic sequencing data from ribosome profiling experiments.")
 606     (license license:gpl3)))
 607
 608 (define-public r-interactionset
 609   (package
 610     (name "r-interactionset")
 611     (version "1.8.0")
 612     (source
 613      (origin
 614        (method url-fetch)
 615        (uri (bioconductor-uri "InteractionSet" version))
 616        (sha256
 617         (base32
 618          "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
 619     (properties
 620      `((upstream-name . "InteractionSet")))
 621     (build-system r-build-system)
 622     (propagated-inputs
 623      `(("r-biocgenerics" ,r-biocgenerics)
 624        ("r-genomeinfodb" ,r-genomeinfodb)
 625        ("r-genomicranges" ,r-genomicranges)
 626        ("r-iranges" ,r-iranges)
 627        ("r-matrix" ,r-matrix)
 628        ("r-rcpp" ,r-rcpp)
 629        ("r-s4vectors" ,r-s4vectors)
 630        ("r-summarizedexperiment" ,r-summarizedexperiment)))
 631     (home-page "https://bioconductor.org/packages/InteractionSet")
 632     (synopsis "Base classes for storing genomic interaction data")
 633     (description
 634      "This packages provides the @code{GInteractions},
 635 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
 636 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
 637 experiments.")
 638     (license license:gpl3)))
 639
 640 (define-public r-genomicinteractions
 641   (package
 642     (name "r-genomicinteractions")
 643     (version "1.14.0")
 644     (source
 645      (origin
 646        (method url-fetch)
 647        (uri (bioconductor-uri "GenomicInteractions" version))
 648        (sha256
 649         (base32
 650          "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
 651     (properties
 652      `((upstream-name . "GenomicInteractions")))
 653     (build-system r-build-system)
 654     (propagated-inputs
 655      `(("r-biobase" ,r-biobase)
 656        ("r-biocgenerics" ,r-biocgenerics)
 657        ("r-data-table" ,r-data-table)
 658        ("r-dplyr" ,r-dplyr)
 659        ("r-genomeinfodb" ,r-genomeinfodb)
 660        ("r-genomicranges" ,r-genomicranges)
 661        ("r-ggplot2" ,r-ggplot2)
 662        ("r-gridextra" ,r-gridextra)
 663        ("r-gviz" ,r-gviz)
 664        ("r-igraph" ,r-igraph)
 665        ("r-interactionset" ,r-interactionset)
 666        ("r-iranges" ,r-iranges)
 667        ("r-rsamtools" ,r-rsamtools)
 668        ("r-rtracklayer" ,r-rtracklayer)
 669        ("r-s4vectors" ,r-s4vectors)
 670        ("r-stringr" ,r-stringr)))
 671     (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
 672     (synopsis "R package for handling genomic interaction data")
 673     (description
 674      "This R package provides tools for handling genomic interaction data,
 675 such as ChIA-PET/Hi-C, annotating genomic features with interaction
 676 information and producing various plots and statistics.")
 677     (license license:gpl3)))