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 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 \f
 201 (define-public r-hpar
 202   (package
 203     (name "r-hpar")
 204     (version "1.24.0")
 205     (source
 206      (origin
 207        (method url-fetch)
 208        (uri (bioconductor-uri "hpar" version))
 209        (sha256
 210         (base32
 211          "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
 212     (build-system r-build-system)
 213     (home-page "https://bioconductor.org/packages/hpar/")
 214     (synopsis "Human Protein Atlas in R")
 215     (description "This package provides a simple interface to and data from
 216 the Human Protein Atlas project.")
 217     (license license:artistic2.0)))
 218
 219 (define-public r-regioner
 220   (package
 221     (name "r-regioner")
 222     (version "1.12.0")
 223     (source
 224      (origin
 225        (method url-fetch)
 226        (uri (bioconductor-uri "regioneR" version))
 227        (sha256
 228         (base32
 229          "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
 230     (properties `((upstream-name . "regioneR")))
 231     (build-system r-build-system)
 232     (propagated-inputs
 233      `(("r-memoise" ,r-memoise)
 234        ("r-genomicranges" ,r-genomicranges)
 235        ("r-bsgenome" ,r-bsgenome)
 236        ("r-rtracklayer" ,r-rtracklayer)
 237        ("r-genomeinfodb" ,r-genomeinfodb)
 238        ("r-iranges" ,r-iranges)
 239        ("r-s4vectors" ,r-s4vectors)))
 240     (home-page "https://bioconductor.org/packages/regioneR/")
 241     (synopsis "Association analysis of genomic regions")
 242     (description "This package offers a statistical framework based on
 243 customizable permutation tests to assess the association between genomic
 244 region sets and other genomic features.")
 245     (license license:artistic2.0)))
 246
 247 (define-public r-diffbind
 248   (package
 249     (name "r-diffbind")
 250     (version "2.10.0")
 251     (source
 252      (origin
 253        (method url-fetch)
 254        (uri (bioconductor-uri "DiffBind" version))
 255        (sha256
 256         (base32
 257          "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
 258     (properties `((upstream-name . "DiffBind")))
 259     (build-system r-build-system)
 260     (inputs
 261      `(("zlib" ,zlib)))
 262     (propagated-inputs
 263      `(("r-amap" ,r-amap)
 264        ("r-biocparallel" ,r-biocparallel)
 265        ("r-deseq2" ,r-deseq2)
 266        ("r-dplyr" ,r-dplyr)
 267        ("r-edger" ,r-edger)
 268        ("r-genomicalignments" ,r-genomicalignments)
 269        ("r-genomicranges" ,r-genomicranges)
 270        ("r-ggplot2" ,r-ggplot2)
 271        ("r-ggrepel" ,r-ggrepel)
 272        ("r-gplots" ,r-gplots)
 273        ("r-iranges" ,r-iranges)
 274        ("r-lattice" ,r-lattice)
 275        ("r-limma" ,r-limma)
 276        ("r-locfit" ,r-locfit)
 277        ("r-rcolorbrewer" , r-rcolorbrewer)
 278        ("r-rcpp" ,r-rcpp)
 279        ("r-rsamtools" ,r-rsamtools)
 280        ("r-s4vectors" ,r-s4vectors)
 281        ("r-summarizedexperiment" ,r-summarizedexperiment)
 282        ("r-systempiper" ,r-systempiper)
 283        ("r-zlibbioc" ,r-zlibbioc)))
 284     (home-page "http://bioconductor.org/packages/DiffBind")
 285     (synopsis "Differential binding analysis of ChIP-Seq peak data")
 286     (description
 287      "This package computes differentially bound sites from multiple
 288 ChIP-seq experiments using affinity (quantitative) data.  Also enables
 289 occupancy (overlap) analysis and plotting functions.")
 290     (license license:artistic2.0)))
 291
 292 (define-public r-ripseeker
 293   (package
 294     (name "r-ripseeker")
 295     (version "1.20.0")
 296     (source
 297      (origin
 298        (method url-fetch)
 299        (uri (bioconductor-uri "RIPSeeker" version))
 300        (sha256
 301         (base32
 302          "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
 303     (properties `((upstream-name . "RIPSeeker")))
 304     (build-system r-build-system)
 305     (propagated-inputs
 306      `(("r-s4vectors" ,r-s4vectors)
 307        ("r-iranges" ,r-iranges)
 308        ("r-genomicranges" ,r-genomicranges)
 309        ("r-summarizedexperiment" ,r-summarizedexperiment)
 310        ("r-rsamtools" ,r-rsamtools)
 311        ("r-genomicalignments" ,r-genomicalignments)
 312        ("r-rtracklayer" ,r-rtracklayer)))
 313     (home-page "http://bioconductor.org/packages/RIPSeeker")
 314     (synopsis
 315      "Identifying protein-associated transcripts from RIP-seq experiments")
 316     (description
 317      "This package infers and discriminates RIP peaks from RIP-seq alignments
 318 using two-state HMM with negative binomial emission probability.  While
 319 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
 320 a suite of bioinformatics tools integrated within this self-contained software
 321 package comprehensively addressing issues ranging from post-alignments
 322 processing to visualization and annotation.")
 323     (license license:gpl2)))
 324
 325 (define-public r-multtest
 326   (package
 327     (name "r-multtest")
 328     (version "2.38.0")
 329     (source
 330      (origin
 331        (method url-fetch)
 332        (uri (bioconductor-uri "multtest" version))
 333        (sha256
 334         (base32
 335          "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
 336     (build-system r-build-system)
 337     (propagated-inputs
 338      `(("r-survival" ,r-survival)
 339        ("r-biocgenerics" ,r-biocgenerics)
 340        ("r-biobase" ,r-biobase)
 341        ("r-mass" ,r-mass)))
 342     (home-page "http://bioconductor.org/packages/multtest")
 343     (synopsis "Resampling-based multiple hypothesis testing")
 344     (description
 345      "This package can do non-parametric bootstrap and permutation
 346 resampling-based multiple testing procedures (including empirical Bayes
 347 methods) for controlling the family-wise error rate (FWER), generalized
 348 family-wise error rate (gFWER), tail probability of the proportion of
 349 false positives (TPPFP), and false discovery rate (FDR).  Several choices
 350 of bootstrap-based null distribution are implemented (centered, centered
 351 and scaled, quantile-transformed).  Single-step and step-wise methods are
 352 available.  Tests based on a variety of T- and F-statistics (including
 353 T-statistics based on regression parameters from linear and survival models
 354 as well as those based on correlation parameters) are included.  When probing
 355 hypotheses with T-statistics, users may also select a potentially faster null
 356 distribution which is multivariate normal with mean zero and variance
 357 covariance matrix derived from the vector influence function.  Results are
 358 reported in terms of adjusted P-values, confidence regions and test statistic
 359 cutoffs.  The procedures are directly applicable to identifying differentially
 360 expressed genes in DNA microarray experiments.")
 361     (license license:lgpl3)))
 362
 363 (define-public r-graph
 364   (package
 365     (name "r-graph")
 366     (version "1.60.0")
 367     (source (origin
 368               (method url-fetch)
 369               (uri (bioconductor-uri "graph" version))
 370               (sha256
 371                (base32
 372                 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
 373     (build-system r-build-system)
 374     (propagated-inputs
 375      `(("r-biocgenerics" ,r-biocgenerics)))
 376     (home-page "https://bioconductor.org/packages/graph")
 377     (synopsis "Handle graph data structures in R")
 378     (description
 379      "This package implements some simple graph handling capabilities for R.")
 380     (license license:artistic2.0)))
 381
 382 (define-public r-codedepends
 383   (package
 384     (name "r-codedepends")
 385     (version "0.6.5")
 386     (source
 387      (origin
 388        (method url-fetch)
 389        (uri (cran-uri "CodeDepends" version))
 390        (sha256
 391         (base32
 392          "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
 393     (properties `((upstream-name . "CodeDepends")))
 394     (build-system r-build-system)
 395     (propagated-inputs
 396      `(("r-codetools" ,r-codetools)
 397        ("r-graph" ,r-graph)
 398        ("r-xml" ,r-xml)))
 399     (home-page "http://cran.r-project.org/web/packages/CodeDepends")
 400     (synopsis "Analysis of R code for reproducible research and code comprehension")
 401     (description
 402      "This package provides tools for analyzing R expressions or blocks of
 403 code and determining the dependencies between them.  It focuses on R scripts,
 404 but can be used on the bodies of functions.  There are many facilities
 405 including the ability to summarize or get a high-level view of code,
 406 determining dependencies between variables, code improvement suggestions.")
 407     ;; Any version of the GPL
 408     (license (list license:gpl2+ license:gpl3+))))
 409
 410 (define-public r-chippeakanno
 411   (package
 412     (name "r-chippeakanno")
 413     (version "3.16.0")
 414     (source
 415      (origin
 416        (method url-fetch)
 417        (uri (bioconductor-uri "ChIPpeakAnno" version))
 418        (sha256
 419         (base32
 420          "09fhh1355diip3v3c0skmp1336vclipkm5nv02qvp5902v4262y3"))))
 421     (properties `((upstream-name . "ChIPpeakAnno")))
 422     (build-system r-build-system)
 423     (propagated-inputs
 424      `(("r-biocgenerics" ,r-biocgenerics)
 425        ("r-biocmanager" ,r-biocmanager)
 426        ("r-biostrings" ,r-biostrings)
 427        ("r-delayedarray" ,r-delayedarray)
 428        ("r-go-db" ,r-go-db)
 429        ("r-biomart" ,r-biomart)
 430        ("r-bsgenome" ,r-bsgenome)
 431        ("r-genomicfeatures" ,r-genomicfeatures)
 432        ("r-genomicranges" ,r-genomicranges)
 433        ("r-genomeinfodb" ,r-genomeinfodb)
 434        ("r-iranges" ,r-iranges)
 435        ("r-matrixstats" ,r-matrixstats)
 436        ("r-annotationdbi" ,r-annotationdbi)
 437        ("r-limma" ,r-limma)
 438        ("r-multtest" ,r-multtest)
 439        ("r-rbgl" ,r-rbgl)
 440        ("r-graph" ,r-graph)
 441        ("r-regioner" ,r-regioner)
 442        ("r-dbi" ,r-dbi)
 443        ("r-ensembldb" ,r-ensembldb)
 444        ("r-biobase" ,r-biobase)
 445        ("r-s4vectors" ,r-s4vectors)
 446        ("r-seqinr" ,r-seqinr)
 447        ("r-idr" ,r-idr)
 448        ("r-genomicalignments" ,r-genomicalignments)
 449        ("r-summarizedexperiment" ,r-summarizedexperiment)
 450        ("r-rsamtools" ,r-rsamtools)
 451        ("r-venndiagram" ,r-venndiagram)))
 452     (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
 453     (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
 454     (description
 455      "The package includes functions to retrieve the sequences around the peak,
 456 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
 457 custom features such as most conserved elements and other transcription factor
 458 binding sites supplied by users.  Starting 2.0.5, new functions have been added
 459 for finding the peaks with bi-directional promoters with summary statistics
 460 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
 461 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
 462 enrichedGO (addGeneIDs).")
 463     (license license:gpl2+)))
 464
 465 (define-public r-marray
 466   (package
 467     (name "r-marray")
 468     (version "1.60.0")
 469     (source (origin
 470               (method url-fetch)
 471               (uri (bioconductor-uri "marray" version))
 472               (sha256
 473                (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
 474     (build-system r-build-system)
 475     (propagated-inputs
 476      `(("r-limma" ,r-limma)))
 477     (home-page "http://bioconductor.org/packages/marray")
 478     (synopsis "Exploratory analysis for two-color spotted microarray data")
 479     (description "This package contains class definitions for two-color spotted
 480 microarray data.  It also includes fuctions for data input, diagnostic plots,
 481 normalization and quality checking.")
 482     (license license:lgpl2.0+)))
 483
 484 (define-public r-cghbase
 485   (package
 486    (name "r-cghbase")
 487    (version "1.42.0")
 488    (source (origin
 489             (method url-fetch)
 490             (uri (bioconductor-uri "CGHbase" version))
 491             (sha256
 492              (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
 493    (properties `((upstream-name . "CGHbase")))
 494    (build-system r-build-system)
 495    (propagated-inputs
 496     `(("r-biobase" ,r-biobase)
 497       ("r-marray" ,r-marray)))
 498    (home-page "http://bioconductor.org/packages/CGHbase")
 499    (synopsis "Base functions and classes for arrayCGH data analysis")
 500    (description "This package contains functions and classes that are needed by
 501 the @code{arrayCGH} packages.")
 502    (license license:gpl2+)))
 503
 504 (define-public r-cghcall
 505   (package
 506    (name "r-cghcall")
 507    (version "2.44.0")
 508    (source (origin
 509             (method url-fetch)
 510             (uri (bioconductor-uri "CGHcall" version))
 511             (sha256
 512              (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
 513    (properties `((upstream-name . "CGHcall")))
 514    (build-system r-build-system)
 515    (propagated-inputs
 516     `(("r-biobase" ,r-biobase)
 517       ("r-cghbase" ,r-cghbase)
 518       ("r-impute" ,r-impute)
 519       ("r-dnacopy" ,r-dnacopy)
 520       ("r-snowfall" ,r-snowfall)))
 521    (home-page "http://bioconductor.org/packages/CGHcall")
 522    (synopsis "Base functions and classes for arrayCGH data analysis")
 523    (description "This package contains functions and classes that are needed by
 524 @code{arrayCGH} packages.")
 525    (license license:gpl2+)))
 526
 527 (define-public r-qdnaseq
 528   (package
 529     (name "r-qdnaseq")
 530     (version "1.18.0")
 531     (source (origin
 532               (method url-fetch)
 533               (uri (bioconductor-uri "QDNAseq" version))
 534               (sha256
 535                (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
 536     (properties `((upstream-name . "QDNAseq")))
 537     (build-system r-build-system)
 538     (propagated-inputs
 539      `(("r-biobase" ,r-biobase)
 540        ("r-biocparallel" ,r-biocparallel)
 541        ("r-cghbase" ,r-cghbase)
 542        ("r-cghcall" ,r-cghcall)
 543        ("r-dnacopy" ,r-dnacopy)
 544        ("r-genomicranges" ,r-genomicranges)
 545        ("r-iranges" ,r-iranges)
 546        ("r-matrixstats" ,r-matrixstats)
 547        ("r-r-utils" ,r-r-utils)
 548        ("r-rsamtools" ,r-rsamtools)))
 549     (home-page "http://bioconductor.org/packages/QDNAseq")
 550     (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
 551     (description "The genome is divided into non-overlapping fixed-sized bins,
 552 number of sequence reads in each counted, adjusted with a simultaneous
 553 two-dimensional loess correction for sequence mappability and GC content, and
 554 filtered to remove spurious regions in the genome.  Downstream steps of
 555 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
 556 respectively.")
 557     (license license:gpl2+)))
 558
 559 (define-public r-bayseq
 560   (package
 561     (name "r-bayseq")
 562     (version "2.14.0")
 563     (source
 564      (origin
 565        (method url-fetch)
 566        (uri (bioconductor-uri "baySeq" version))
 567        (sha256
 568         (base32
 569          "0hbmm01a8libara9mbxknpk0wzarwfngnfwlmhpww91a0cmy5klg"))))
 570     (properties `((upstream-name . "baySeq")))
 571     (build-system r-build-system)
 572     (propagated-inputs
 573      `(("r-abind" ,r-abind)
 574        ("r-edger" ,r-edger)
 575        ("r-genomicranges" ,r-genomicranges)))
 576     (home-page "https://bioconductor.org/packages/baySeq/")
 577     (synopsis "Bayesian analysis of differential expression patterns in count data")
 578     (description
 579      "This package identifies differential expression in high-throughput count
 580 data, such as that derived from next-generation sequencing machines,
 581 calculating estimated posterior likelihoods of differential expression (or
 582 more complex hypotheses) via empirical Bayesian methods.")
 583     (license license:gpl3)))
 584
 585 (define-public r-chipcomp
 586   (package
 587     (name "r-chipcomp")
 588     (version "1.10.0")
 589     (source
 590      (origin
 591        (method url-fetch)
 592        (uri (bioconductor-uri "ChIPComp" version))
 593        (sha256
 594         (base32
 595          "0j9nif7z33qdxf347r9wa62hhz8qs09r2p96x3hg5yz30a10ahqs"))))
 596     (properties `((upstream-name . "ChIPComp")))
 597     (build-system r-build-system)
 598     (propagated-inputs
 599      `(("r-biocgenerics" ,r-biocgenerics)
 600        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
 601        ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
 602        ("r-genomeinfodb" ,r-genomeinfodb)
 603        ("r-genomicranges" ,r-genomicranges)
 604        ("r-iranges" ,r-iranges)
 605        ("r-limma" ,r-limma)
 606        ("r-rsamtools" ,r-rsamtools)
 607        ("r-rtracklayer" ,r-rtracklayer)
 608        ("r-s4vectors" ,r-s4vectors)))
 609     (home-page "https://bioconductor.org/packages/ChIPComp")
 610     (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
 611     (description
 612      "ChIPComp implements a statistical method for quantitative comparison of
 613 multiple ChIP-seq datasets.  It detects differentially bound sharp binding
 614 sites across multiple conditions considering matching control in ChIP-seq
 615 datasets.")
 616     ;; Any version of the GPL.
 617     (license license:gpl3+)))
 618
 619 (define-public r-riboprofiling
 620   (package
 621     (name "r-riboprofiling")
 622     (version "1.10.0")
 623     (source
 624      (origin
 625        (method url-fetch)
 626        (uri (bioconductor-uri "RiboProfiling" version))
 627        (sha256
 628         (base32
 629          "04yjklqdjkim7yxyk3cyvf0mmwyxyfvw2mmfzgwaaqbiyg29sli0"))))
 630     (properties `((upstream-name . "RiboProfiling")))
 631     (build-system r-build-system)
 632     (propagated-inputs
 633      `(("r-biocgenerics" ,r-biocgenerics)
 634        ("r-biostrings" ,r-biostrings)
 635        ("r-data-table" ,r-data-table)
 636        ("r-genomeinfodb" ,r-genomeinfodb)
 637        ("r-genomicalignments" ,r-genomicalignments)
 638        ("r-genomicfeatures" ,r-genomicfeatures)
 639        ("r-genomicranges" ,r-genomicranges)
 640        ("r-ggbio" ,r-ggbio)
 641        ("r-ggplot2" ,r-ggplot2)
 642        ("r-iranges" ,r-iranges)
 643        ("r-plyr" ,r-plyr)
 644        ("r-reshape2" ,r-reshape2)
 645        ("r-rsamtools" ,r-rsamtools)
 646        ("r-rtracklayer" ,r-rtracklayer)
 647        ("r-s4vectors" ,r-s4vectors)
 648        ("r-sqldf" ,r-sqldf)))
 649     (home-page "https://bioconductor.org/packages/RiboProfiling/")
 650     (synopsis "Ribosome profiling data analysis")
 651     (description "Starting with a BAM file, this package provides the
 652 necessary functions for quality assessment, read start position recalibration,
 653 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
 654 of count data: pairs, log fold-change, codon frequency and coverage
 655 assessment, principal component analysis on codon coverage.")
 656     (license license:gpl3)))
 657
 658 (define-public r-riboseqr
 659   (package
 660     (name "r-riboseqr")
 661     (version "1.14.0")
 662     (source
 663      (origin
 664        (method url-fetch)
 665        (uri (bioconductor-uri "riboSeqR" version))
 666        (sha256
 667         (base32
 668          "0xavd1cdhi8qfjn9a1hjhflyg6jq1ydvv56z12gjz572pwz2knvn"))))
 669     (properties `((upstream-name . "riboSeqR")))
 670     (build-system r-build-system)
 671     (propagated-inputs
 672      `(("r-abind" ,r-abind)
 673        ("r-bayseq" ,r-bayseq)
 674        ("r-genomeinfodb" ,r-genomeinfodb)
 675        ("r-genomicranges" ,r-genomicranges)
 676        ("r-iranges" ,r-iranges)
 677        ("r-rsamtools" ,r-rsamtools)
 678        ("r-seqlogo" ,r-seqlogo)))
 679     (home-page "https://bioconductor.org/packages/riboSeqR/")
 680     (synopsis "Analysis of sequencing data from ribosome profiling experiments")
 681     (description
 682      "This package provides plotting functions, frameshift detection and
 683 parsing of genetic sequencing data from ribosome profiling experiments.")
 684     (license license:gpl3)))
 685
 686 (define-public r-interactionset
 687   (package
 688     (name "r-interactionset")
 689     (version "1.8.0")
 690     (source
 691      (origin
 692        (method url-fetch)
 693        (uri (bioconductor-uri "InteractionSet" version))
 694        (sha256
 695         (base32
 696          "0xngraq7ic80jr98i1wqp8bxdgidq6py60m2wfk82n1ixpcdck8n"))))
 697     (properties
 698      `((upstream-name . "InteractionSet")))
 699     (build-system r-build-system)
 700     (propagated-inputs
 701      `(("r-biocgenerics" ,r-biocgenerics)
 702        ("r-genomeinfodb" ,r-genomeinfodb)
 703        ("r-genomicranges" ,r-genomicranges)
 704        ("r-iranges" ,r-iranges)
 705        ("r-matrix" ,r-matrix)
 706        ("r-rcpp" ,r-rcpp)
 707        ("r-s4vectors" ,r-s4vectors)
 708        ("r-summarizedexperiment" ,r-summarizedexperiment)))
 709     (home-page "https://bioconductor.org/packages/InteractionSet")
 710     (synopsis "Base classes for storing genomic interaction data")
 711     (description
 712      "This packages provides the @code{GInteractions},
 713 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
 714 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
 715 experiments.")
 716     (license license:gpl3)))
 717
 718 (define-public r-genomicinteractions
 719   (package
 720     (name "r-genomicinteractions")
 721     (version "1.14.0")
 722     (source
 723      (origin
 724        (method url-fetch)
 725        (uri (bioconductor-uri "GenomicInteractions" version))
 726        (sha256
 727         (base32
 728          "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
 729     (properties
 730      `((upstream-name . "GenomicInteractions")))
 731     (build-system r-build-system)
 732     (propagated-inputs
 733      `(("r-biobase" ,r-biobase)
 734        ("r-biocgenerics" ,r-biocgenerics)
 735        ("r-data-table" ,r-data-table)
 736        ("r-dplyr" ,r-dplyr)
 737        ("r-genomeinfodb" ,r-genomeinfodb)
 738        ("r-genomicranges" ,r-genomicranges)
 739        ("r-ggplot2" ,r-ggplot2)
 740        ("r-gridextra" ,r-gridextra)
 741        ("r-gviz" ,r-gviz)
 742        ("r-igraph" ,r-igraph)
 743        ("r-interactionset" ,r-interactionset)
 744        ("r-iranges" ,r-iranges)
 745        ("r-rsamtools" ,r-rsamtools)
 746        ("r-rtracklayer" ,r-rtracklayer)
 747        ("r-s4vectors" ,r-s4vectors)
 748        ("r-stringr" ,r-stringr)))
 749     (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
 750     (synopsis "R package for handling genomic interaction data")
 751     (description
 752      "This R package provides tools for handling genomic interaction data,
 753 such as ChIA-PET/Hi-C, annotating genomic features with interaction
 754 information and producing various plots and statistics.")
 755     (license license:gpl3)))
 756
 757 (define-public r-ctc
 758   (package
 759     (name "r-ctc")
 760     (version "1.54.0")
 761     (source
 762      (origin
 763        (method url-fetch)
 764        (uri (bioconductor-uri "ctc" version))
 765        (sha256
 766         (base32
 767          "0sadplm4n9n3z6inmn6y3d6qbr4hllljqh700x5fygrnfacnckk9"))))
 768     (build-system r-build-system)
 769     (propagated-inputs `(("r-amap" ,r-amap)))
 770     (home-page "https://bioconductor.org/packages/ctc/")
 771     (synopsis "Cluster and tree conversion")
 772     (description
 773      "This package provides tools for exporting and importing classification
 774 trees and clusters to other programs.")
 775     (license license:gpl2)))
 776
 777 (define-public r-goseq
 778   (package
 779     (name "r-goseq")
 780     (version "1.32.0")
 781     (source
 782      (origin
 783        (method url-fetch)
 784        (uri (bioconductor-uri "goseq" version))
 785        (sha256
 786         (base32
 787          "0xmbb8ma32lrfy810r82y34gkspq4fqiqxykic9j4rq9rg9n9x2l"))))
 788     (build-system r-build-system)
 789     (propagated-inputs
 790      `(("r-annotationdbi" ,r-annotationdbi)
 791        ("r-biasedurn" ,r-biasedurn)
 792        ("r-biocgenerics" ,r-biocgenerics)
 793        ("r-genelendatabase" ,r-genelendatabase)
 794        ("r-go-db" ,r-go-db)
 795        ("r-mgcv" ,r-mgcv)))
 796     (home-page "https://bioconductor.org/packages/goseq/")
 797     (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
 798     (description
 799      "This package provides tools to detect Gene Ontology and/or other user
 800 defined categories which are over/under represented in RNA-seq data.")
 801     (license license:lgpl2.0+)))
 802
 803 (define-public r-glimma
 804   (package
 805     (name "r-glimma")
 806     (version "1.8.2")
 807     (source
 808      (origin
 809        (method url-fetch)
 810        (uri (bioconductor-uri "Glimma" version))
 811        (sha256
 812         (base32
 813          "0kfia60vrlys6amdchdix01iwbkwyb7nfjqn5hczsxp8rhmbg25s"))))
 814     (properties `((upstream-name . "Glimma")))
 815     (build-system r-build-system)
 816     (propagated-inputs
 817      `(("r-edger" ,r-edger)
 818        ("r-jsonlite" ,r-jsonlite)
 819        ("r-s4vectors" ,r-s4vectors)))
 820     (home-page "https://github.com/Shians/Glimma")
 821     (synopsis "Interactive HTML graphics")
 822     (description
 823      "This package generates interactive visualisations for analysis of
 824 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
 825 HTML page.  The interactions are built on top of the popular static
 826 representations of analysis results in order to provide additional
 827 information.")
 828     (license license:lgpl3)))
 829
 830 (define-public r-rots
 831   (package
 832     (name "r-rots")
 833     (version "1.8.0")
 834     (source
 835      (origin
 836        (method url-fetch)
 837        (uri (bioconductor-uri "ROTS" version))
 838        (sha256
 839         (base32
 840          "12jvdqanyk86ihpcylp105zip22y0gkbksmyxy00q7iad0jhaqp3"))))
 841     (properties `((upstream-name . "ROTS")))
 842     (build-system r-build-system)
 843     (propagated-inputs
 844      `(("r-biobase" ,r-biobase)
 845        ("r-rcpp" ,r-rcpp)))
 846     (home-page "https://bioconductor.org/packages/ROTS/")
 847     (synopsis "Reproducibility-Optimized Test Statistic")
 848     (description
 849      "This package provides tools for calculating the
 850 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
 851 in omics data.")
 852     (license license:gpl2+)))
 853
 854 (define-public r-inspect
 855   (package
 856     (name "r-inspect")
 857     (version "1.10.0")
 858     (source
 859      (origin
 860        (method url-fetch)
 861        (uri (bioconductor-uri "INSPEcT" version))
 862        (sha256
 863         (base32
 864          "1gk0pwyimkswrvgb2xr3c2zy4myi448a2shr5ap65rq9pcpp0l8p"))))
 865     (properties `((upstream-name . "INSPEcT")))
 866     (build-system r-build-system)
 867     (propagated-inputs
 868      `(("r-biobase" ,r-biobase)
 869        ("r-biocgenerics" ,r-biocgenerics)
 870        ("r-biocparallel" ,r-biocparallel)
 871        ("r-desolve" ,r-desolve)
 872        ("r-genomicalignments" ,r-genomicalignments)
 873        ("r-genomicfeatures" ,r-genomicfeatures)
 874        ("r-genomicranges" ,r-genomicranges)
 875        ("r-iranges" ,r-iranges)
 876        ("r-preprocesscore" ,r-preprocesscore)
 877        ("r-proc" ,r-proc)
 878        ("r-rootsolve" ,r-rootsolve)
 879        ("r-rsamtools" ,r-rsamtools)
 880        ("r-s4vectors" ,r-s4vectors)))
 881     (home-page "https://bioconductor.org/packages/INSPEcT")
 882     (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
 883     (description
 884      "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
 885 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
 886 order to evaluate synthesis, processing and degradation rates and assess via
 887 modeling the rates that determines changes in mature mRNA levels.")
 888     (license license:gpl2)))
 889
 890 (define-public r-dnabarcodes
 891   (package
 892     (name "r-dnabarcodes")
 893     (version "1.10.0")
 894     (source
 895      (origin
 896        (method url-fetch)
 897        (uri (bioconductor-uri "DNABarcodes" version))
 898        (sha256
 899         (base32
 900          "0xhna7f0kr7pp2hqwara5i57m9mdr65shflfxiyw6yy3g90pgb5x"))))
 901     (properties `((upstream-name . "DNABarcodes")))
 902     (build-system r-build-system)
 903     (propagated-inputs
 904      `(("r-bh" ,r-bh)
 905        ("r-matrix" ,r-matrix)
 906        ("r-rcpp" ,r-rcpp)))
 907     (home-page "https://bioconductor.org/packages/DNABarcodes")
 908     (synopsis "Create and analyze DNA barcodes")
 909     (description
 910      "This package offers tools to create DNA barcode sets capable of
 911 correcting insertion, deletion, and substitution errors.  Existing barcodes
 912 can be analyzed regarding their minimal, maximal and average distances between
 913 barcodes.  Finally, reads that start with a (possibly mutated) barcode can be
 914 demultiplexed, i.e. assigned to their original reference barcode.")
 915     (license license:gpl2)))
 916
 917 (define-public r-ruvseq
 918   (package
 919     (name "r-ruvseq")
 920     (version "1.14.0")
 921     (source
 922      (origin
 923        (method url-fetch)
 924        (uri (bioconductor-uri "RUVSeq" version))
 925        (sha256
 926         (base32
 927          "16i5sm5af761k4zvspfi8jknsgln48bn538hxqqmlaq7wvlfxqxj"))))
 928     (properties `((upstream-name . "RUVSeq")))
 929     (build-system r-build-system)
 930     (propagated-inputs
 931      `(("r-biobase" ,r-biobase)
 932        ("r-edaseq" ,r-edaseq)
 933        ("r-edger" ,r-edger)
 934        ("r-mass" ,r-mass)))
 935     (home-page "https://github.com/drisso/RUVSeq")
 936     (synopsis "Remove unwanted variation from RNA-Seq data")
 937     (description
 938      "This package implements methods to @dfn{remove unwanted variation} (RUV)
 939 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
 940 samples.")
 941     (license license:artistic2.0)))