gnu/packages/bioconductor.scm

   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-biocgenerics
 232   (package
 233     (name "r-biocgenerics")
 234     (version "0.28.0")
 235     (source (origin
 236               (method url-fetch)
 237               (uri (bioconductor-uri "BiocGenerics" version))
 238               (sha256
 239                (base32
 240                 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
 241     (properties
 242      `((upstream-name . "BiocGenerics")))
 243     (build-system r-build-system)
 244     (home-page "https://bioconductor.org/packages/BiocGenerics")
 245     (synopsis "S4 generic functions for Bioconductor")
 246     (description
 247      "This package provides S4 generic functions needed by many Bioconductor
 248 packages.")
 249     (license license:artistic2.0)))
 250
 251 (define-public r-annotate
 252   (package
 253     (name "r-annotate")
 254     (version "1.60.0")
 255     (source
 256      (origin
 257        (method url-fetch)
 258        (uri (bioconductor-uri "annotate" version))
 259        (sha256
 260         (base32
 261          "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
 262     (build-system r-build-system)
 263     (propagated-inputs
 264      `(("r-annotationdbi" ,r-annotationdbi)
 265        ("r-biobase" ,r-biobase)
 266        ("r-biocgenerics" ,r-biocgenerics)
 267        ("r-dbi" ,r-dbi)
 268        ("r-rcurl" ,r-rcurl)
 269        ("r-xml" ,r-xml)
 270        ("r-xtable" ,r-xtable)))
 271     (home-page
 272      "https://bioconductor.org/packages/annotate")
 273     (synopsis "Annotation for microarrays")
 274     (description "This package provides R environments for the annotation of
 275 microarrays.")
 276     (license license:artistic2.0)))
 277
 278 (define-public r-hpar
 279   (package
 280     (name "r-hpar")
 281     (version "1.24.0")
 282     (source
 283      (origin
 284        (method url-fetch)
 285        (uri (bioconductor-uri "hpar" version))
 286        (sha256
 287         (base32
 288          "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
 289     (build-system r-build-system)
 290     (home-page "https://bioconductor.org/packages/hpar/")
 291     (synopsis "Human Protein Atlas in R")
 292     (description "This package provides a simple interface to and data from
 293 the Human Protein Atlas project.")
 294     (license license:artistic2.0)))
 295
 296 (define-public r-regioner
 297   (package
 298     (name "r-regioner")
 299     (version "1.14.0")
 300     (source
 301      (origin
 302        (method url-fetch)
 303        (uri (bioconductor-uri "regioneR" version))
 304        (sha256
 305         (base32
 306          "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
 307     (properties `((upstream-name . "regioneR")))
 308     (build-system r-build-system)
 309     (propagated-inputs
 310      `(("r-biostrings" ,r-biostrings)
 311        ("r-bsgenome" ,r-bsgenome)
 312        ("r-genomeinfodb" ,r-genomeinfodb)
 313        ("r-genomicranges" ,r-genomicranges)
 314        ("r-iranges" ,r-iranges)
 315        ("r-memoise" ,r-memoise)
 316        ("r-rtracklayer" ,r-rtracklayer)
 317        ("r-s4vectors" ,r-s4vectors)))
 318     (home-page "https://bioconductor.org/packages/regioneR/")
 319     (synopsis "Association analysis of genomic regions")
 320     (description "This package offers a statistical framework based on
 321 customizable permutation tests to assess the association between genomic
 322 region sets and other genomic features.")
 323     (license license:artistic2.0)))
 324
 325 (define-public r-diffbind
 326   (package
 327     (name "r-diffbind")
 328     (version "2.10.0")
 329     (source
 330      (origin
 331        (method url-fetch)
 332        (uri (bioconductor-uri "DiffBind" version))
 333        (sha256
 334         (base32
 335          "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
 336     (properties `((upstream-name . "DiffBind")))
 337     (build-system r-build-system)
 338     (inputs
 339      `(("zlib" ,zlib)))
 340     (propagated-inputs
 341      `(("r-amap" ,r-amap)
 342        ("r-biocparallel" ,r-biocparallel)
 343        ("r-deseq2" ,r-deseq2)
 344        ("r-dplyr" ,r-dplyr)
 345        ("r-edger" ,r-edger)
 346        ("r-genomicalignments" ,r-genomicalignments)
 347        ("r-genomicranges" ,r-genomicranges)
 348        ("r-ggplot2" ,r-ggplot2)
 349        ("r-ggrepel" ,r-ggrepel)
 350        ("r-gplots" ,r-gplots)
 351        ("r-iranges" ,r-iranges)
 352        ("r-lattice" ,r-lattice)
 353        ("r-limma" ,r-limma)
 354        ("r-locfit" ,r-locfit)
 355        ("r-rcolorbrewer" , r-rcolorbrewer)
 356        ("r-rcpp" ,r-rcpp)
 357        ("r-rsamtools" ,r-rsamtools)
 358        ("r-s4vectors" ,r-s4vectors)
 359        ("r-summarizedexperiment" ,r-summarizedexperiment)
 360        ("r-systempiper" ,r-systempiper)
 361        ("r-zlibbioc" ,r-zlibbioc)))
 362     (home-page "http://bioconductor.org/packages/DiffBind")
 363     (synopsis "Differential binding analysis of ChIP-Seq peak data")
 364     (description
 365      "This package computes differentially bound sites from multiple
 366 ChIP-seq experiments using affinity (quantitative) data.  Also enables
 367 occupancy (overlap) analysis and plotting functions.")
 368     (license license:artistic2.0)))
 369
 370 (define-public r-ripseeker
 371   (package
 372     (name "r-ripseeker")
 373     (version "1.22.0")
 374     (source
 375      (origin
 376        (method url-fetch)
 377        (uri (bioconductor-uri "RIPSeeker" version))
 378        (sha256
 379         (base32
 380          "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
 381     (properties `((upstream-name . "RIPSeeker")))
 382     (build-system r-build-system)
 383     (propagated-inputs
 384      `(("r-s4vectors" ,r-s4vectors)
 385        ("r-iranges" ,r-iranges)
 386        ("r-genomicranges" ,r-genomicranges)
 387        ("r-summarizedexperiment" ,r-summarizedexperiment)
 388        ("r-rsamtools" ,r-rsamtools)
 389        ("r-genomicalignments" ,r-genomicalignments)
 390        ("r-rtracklayer" ,r-rtracklayer)))
 391     (home-page "http://bioconductor.org/packages/RIPSeeker")
 392     (synopsis
 393      "Identifying protein-associated transcripts from RIP-seq experiments")
 394     (description
 395      "This package infers and discriminates RIP peaks from RIP-seq alignments
 396 using two-state HMM with negative binomial emission probability.  While
 397 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
 398 a suite of bioinformatics tools integrated within this self-contained software
 399 package comprehensively addressing issues ranging from post-alignments
 400 processing to visualization and annotation.")
 401     (license license:gpl2)))
 402
 403 (define-public r-multtest
 404   (package
 405     (name "r-multtest")
 406     (version "2.38.0")
 407     (source
 408      (origin
 409        (method url-fetch)
 410        (uri (bioconductor-uri "multtest" version))
 411        (sha256
 412         (base32
 413          "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
 414     (build-system r-build-system)
 415     (propagated-inputs
 416      `(("r-survival" ,r-survival)
 417        ("r-biocgenerics" ,r-biocgenerics)
 418        ("r-biobase" ,r-biobase)
 419        ("r-mass" ,r-mass)))
 420     (home-page "http://bioconductor.org/packages/multtest")
 421     (synopsis "Resampling-based multiple hypothesis testing")
 422     (description
 423      "This package can do non-parametric bootstrap and permutation
 424 resampling-based multiple testing procedures (including empirical Bayes
 425 methods) for controlling the family-wise error rate (FWER), generalized
 426 family-wise error rate (gFWER), tail probability of the proportion of
 427 false positives (TPPFP), and false discovery rate (FDR).  Several choices
 428 of bootstrap-based null distribution are implemented (centered, centered
 429 and scaled, quantile-transformed).  Single-step and step-wise methods are
 430 available.  Tests based on a variety of T- and F-statistics (including
 431 T-statistics based on regression parameters from linear and survival models
 432 as well as those based on correlation parameters) are included.  When probing
 433 hypotheses with T-statistics, users may also select a potentially faster null
 434 distribution which is multivariate normal with mean zero and variance
 435 covariance matrix derived from the vector influence function.  Results are
 436 reported in terms of adjusted P-values, confidence regions and test statistic
 437 cutoffs.  The procedures are directly applicable to identifying differentially
 438 expressed genes in DNA microarray experiments.")
 439     (license license:lgpl3)))
 440
 441 (define-public r-graph
 442   (package
 443     (name "r-graph")
 444     (version "1.60.0")
 445     (source (origin
 446               (method url-fetch)
 447               (uri (bioconductor-uri "graph" version))
 448               (sha256
 449                (base32
 450                 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
 451     (build-system r-build-system)
 452     (propagated-inputs
 453      `(("r-biocgenerics" ,r-biocgenerics)))
 454     (home-page "https://bioconductor.org/packages/graph")
 455     (synopsis "Handle graph data structures in R")
 456     (description
 457      "This package implements some simple graph handling capabilities for R.")
 458     (license license:artistic2.0)))
 459
 460 (define-public r-codedepends
 461   (package
 462     (name "r-codedepends")
 463     (version "0.6.5")
 464     (source
 465      (origin
 466        (method url-fetch)
 467        (uri (cran-uri "CodeDepends" version))
 468        (sha256
 469         (base32
 470          "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
 471     (properties `((upstream-name . "CodeDepends")))
 472     (build-system r-build-system)
 473     (propagated-inputs
 474      `(("r-codetools" ,r-codetools)
 475        ("r-graph" ,r-graph)
 476        ("r-xml" ,r-xml)))
 477     (home-page "http://cran.r-project.org/web/packages/CodeDepends")
 478     (synopsis "Analysis of R code for reproducible research and code comprehension")
 479     (description
 480      "This package provides tools for analyzing R expressions or blocks of
 481 code and determining the dependencies between them.  It focuses on R scripts,
 482 but can be used on the bodies of functions.  There are many facilities
 483 including the ability to summarize or get a high-level view of code,
 484 determining dependencies between variables, code improvement suggestions.")
 485     ;; Any version of the GPL
 486     (license (list license:gpl2+ license:gpl3+))))
 487
 488 (define-public r-chippeakanno
 489   (package
 490     (name "r-chippeakanno")
 491     (version "3.16.1")
 492     (source
 493      (origin
 494        (method url-fetch)
 495        (uri (bioconductor-uri "ChIPpeakAnno" version))
 496        (sha256
 497         (base32
 498          "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
 499     (properties `((upstream-name . "ChIPpeakAnno")))
 500     (build-system r-build-system)
 501     (propagated-inputs
 502      `(("r-biocgenerics" ,r-biocgenerics)
 503        ("r-biocmanager" ,r-biocmanager)
 504        ("r-biostrings" ,r-biostrings)
 505        ("r-delayedarray" ,r-delayedarray)
 506        ("r-go-db" ,r-go-db)
 507        ("r-biomart" ,r-biomart)
 508        ("r-bsgenome" ,r-bsgenome)
 509        ("r-genomicfeatures" ,r-genomicfeatures)
 510        ("r-genomicranges" ,r-genomicranges)
 511        ("r-genomeinfodb" ,r-genomeinfodb)
 512        ("r-iranges" ,r-iranges)
 513        ("r-matrixstats" ,r-matrixstats)
 514        ("r-annotationdbi" ,r-annotationdbi)
 515        ("r-limma" ,r-limma)
 516        ("r-multtest" ,r-multtest)
 517        ("r-rbgl" ,r-rbgl)
 518        ("r-graph" ,r-graph)
 519        ("r-regioner" ,r-regioner)
 520        ("r-dbi" ,r-dbi)
 521        ("r-ensembldb" ,r-ensembldb)
 522        ("r-biobase" ,r-biobase)
 523        ("r-s4vectors" ,r-s4vectors)
 524        ("r-seqinr" ,r-seqinr)
 525        ("r-idr" ,r-idr)
 526        ("r-genomicalignments" ,r-genomicalignments)
 527        ("r-summarizedexperiment" ,r-summarizedexperiment)
 528        ("r-rsamtools" ,r-rsamtools)
 529        ("r-venndiagram" ,r-venndiagram)))
 530     (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
 531     (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
 532     (description
 533      "The package includes functions to retrieve the sequences around the peak,
 534 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
 535 custom features such as most conserved elements and other transcription factor
 536 binding sites supplied by users.  Starting 2.0.5, new functions have been added
 537 for finding the peaks with bi-directional promoters with summary statistics
 538 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
 539 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
 540 enrichedGO (addGeneIDs).")
 541     (license license:gpl2+)))
 542
 543 (define-public r-marray
 544   (package
 545     (name "r-marray")
 546     (version "1.60.0")
 547     (source (origin
 548               (method url-fetch)
 549               (uri (bioconductor-uri "marray" version))
 550               (sha256
 551                (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
 552     (build-system r-build-system)
 553     (propagated-inputs
 554      `(("r-limma" ,r-limma)))
 555     (home-page "http://bioconductor.org/packages/marray")
 556     (synopsis "Exploratory analysis for two-color spotted microarray data")
 557     (description "This package contains class definitions for two-color spotted
 558 microarray data.  It also includes fuctions for data input, diagnostic plots,
 559 normalization and quality checking.")
 560     (license license:lgpl2.0+)))
 561
 562 (define-public r-cghbase
 563   (package
 564    (name "r-cghbase")
 565    (version "1.42.0")
 566    (source (origin
 567             (method url-fetch)
 568             (uri (bioconductor-uri "CGHbase" version))
 569             (sha256
 570              (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
 571    (properties `((upstream-name . "CGHbase")))
 572    (build-system r-build-system)
 573    (propagated-inputs
 574     `(("r-biobase" ,r-biobase)
 575       ("r-marray" ,r-marray)))
 576    (home-page "http://bioconductor.org/packages/CGHbase")
 577    (synopsis "Base functions and classes for arrayCGH data analysis")
 578    (description "This package contains functions and classes that are needed by
 579 the @code{arrayCGH} packages.")
 580    (license license:gpl2+)))
 581
 582 (define-public r-cghcall
 583   (package
 584    (name "r-cghcall")
 585    (version "2.44.0")
 586    (source (origin
 587             (method url-fetch)
 588             (uri (bioconductor-uri "CGHcall" version))
 589             (sha256
 590              (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
 591    (properties `((upstream-name . "CGHcall")))
 592    (build-system r-build-system)
 593    (propagated-inputs
 594     `(("r-biobase" ,r-biobase)
 595       ("r-cghbase" ,r-cghbase)
 596       ("r-impute" ,r-impute)
 597       ("r-dnacopy" ,r-dnacopy)
 598       ("r-snowfall" ,r-snowfall)))
 599    (home-page "http://bioconductor.org/packages/CGHcall")
 600    (synopsis "Base functions and classes for arrayCGH data analysis")
 601    (description "This package contains functions and classes that are needed by
 602 @code{arrayCGH} packages.")
 603    (license license:gpl2+)))
 604
 605 (define-public r-qdnaseq
 606   (package
 607     (name "r-qdnaseq")
 608     (version "1.18.0")
 609     (source (origin
 610               (method url-fetch)
 611               (uri (bioconductor-uri "QDNAseq" version))
 612               (sha256
 613                (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
 614     (properties `((upstream-name . "QDNAseq")))
 615     (build-system r-build-system)
 616     (propagated-inputs
 617      `(("r-biobase" ,r-biobase)
 618        ("r-biocparallel" ,r-biocparallel)
 619        ("r-cghbase" ,r-cghbase)
 620        ("r-cghcall" ,r-cghcall)
 621        ("r-dnacopy" ,r-dnacopy)
 622        ("r-genomicranges" ,r-genomicranges)
 623        ("r-iranges" ,r-iranges)
 624        ("r-matrixstats" ,r-matrixstats)
 625        ("r-r-utils" ,r-r-utils)
 626        ("r-rsamtools" ,r-rsamtools)))
 627     (home-page "http://bioconductor.org/packages/QDNAseq")
 628     (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
 629     (description "The genome is divided into non-overlapping fixed-sized bins,
 630 number of sequence reads in each counted, adjusted with a simultaneous
 631 two-dimensional loess correction for sequence mappability and GC content, and
 632 filtered to remove spurious regions in the genome.  Downstream steps of
 633 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
 634 respectively.")
 635     (license license:gpl2+)))
 636
 637 (define-public r-bayseq
 638   (package
 639     (name "r-bayseq")
 640     (version "2.16.0")
 641     (source
 642      (origin
 643        (method url-fetch)
 644        (uri (bioconductor-uri "baySeq" version))
 645        (sha256
 646         (base32
 647          "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
 648     (properties `((upstream-name . "baySeq")))
 649     (build-system r-build-system)
 650     (propagated-inputs
 651      `(("r-abind" ,r-abind)
 652        ("r-edger" ,r-edger)
 653        ("r-genomicranges" ,r-genomicranges)))
 654     (home-page "https://bioconductor.org/packages/baySeq/")
 655     (synopsis "Bayesian analysis of differential expression patterns in count data")
 656     (description
 657      "This package identifies differential expression in high-throughput count
 658 data, such as that derived from next-generation sequencing machines,
 659 calculating estimated posterior likelihoods of differential expression (or
 660 more complex hypotheses) via empirical Bayesian methods.")
 661     (license license:gpl3)))
 662
 663 (define-public r-chipcomp
 664   (package
 665     (name "r-chipcomp")
 666     (version "1.12.0")
 667     (source
 668      (origin
 669        (method url-fetch)
 670        (uri (bioconductor-uri "ChIPComp" version))
 671        (sha256
 672         (base32
 673          "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
 674     (properties `((upstream-name . "ChIPComp")))
 675     (build-system r-build-system)
 676     (propagated-inputs
 677      `(("r-biocgenerics" ,r-biocgenerics)
 678        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
 679        ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
 680        ("r-genomeinfodb" ,r-genomeinfodb)
 681        ("r-genomicranges" ,r-genomicranges)
 682        ("r-iranges" ,r-iranges)
 683        ("r-limma" ,r-limma)
 684        ("r-rsamtools" ,r-rsamtools)
 685        ("r-rtracklayer" ,r-rtracklayer)
 686        ("r-s4vectors" ,r-s4vectors)))
 687     (home-page "https://bioconductor.org/packages/ChIPComp")
 688     (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
 689     (description
 690      "ChIPComp implements a statistical method for quantitative comparison of
 691 multiple ChIP-seq datasets.  It detects differentially bound sharp binding
 692 sites across multiple conditions considering matching control in ChIP-seq
 693 datasets.")
 694     ;; Any version of the GPL.
 695     (license license:gpl3+)))
 696
 697 (define-public r-riboprofiling
 698   (package
 699     (name "r-riboprofiling")
 700     (version "1.12.0")
 701     (source
 702      (origin
 703        (method url-fetch)
 704        (uri (bioconductor-uri "RiboProfiling" version))
 705        (sha256
 706         (base32
 707          "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
 708     (properties `((upstream-name . "RiboProfiling")))
 709     (build-system r-build-system)
 710     (propagated-inputs
 711      `(("r-biocgenerics" ,r-biocgenerics)
 712        ("r-biostrings" ,r-biostrings)
 713        ("r-data-table" ,r-data-table)
 714        ("r-genomeinfodb" ,r-genomeinfodb)
 715        ("r-genomicalignments" ,r-genomicalignments)
 716        ("r-genomicfeatures" ,r-genomicfeatures)
 717        ("r-genomicranges" ,r-genomicranges)
 718        ("r-ggbio" ,r-ggbio)
 719        ("r-ggplot2" ,r-ggplot2)
 720        ("r-iranges" ,r-iranges)
 721        ("r-plyr" ,r-plyr)
 722        ("r-reshape2" ,r-reshape2)
 723        ("r-rsamtools" ,r-rsamtools)
 724        ("r-rtracklayer" ,r-rtracklayer)
 725        ("r-s4vectors" ,r-s4vectors)
 726        ("r-sqldf" ,r-sqldf)))
 727     (home-page "https://bioconductor.org/packages/RiboProfiling/")
 728     (synopsis "Ribosome profiling data analysis")
 729     (description "Starting with a BAM file, this package provides the
 730 necessary functions for quality assessment, read start position recalibration,
 731 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
 732 of count data: pairs, log fold-change, codon frequency and coverage
 733 assessment, principal component analysis on codon coverage.")
 734     (license license:gpl3)))
 735
 736 (define-public r-riboseqr
 737   (package
 738     (name "r-riboseqr")
 739     (version "1.16.0")
 740     (source
 741      (origin
 742        (method url-fetch)
 743        (uri (bioconductor-uri "riboSeqR" version))
 744        (sha256
 745         (base32
 746          "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
 747     (properties `((upstream-name . "riboSeqR")))
 748     (build-system r-build-system)
 749     (propagated-inputs
 750      `(("r-abind" ,r-abind)
 751        ("r-bayseq" ,r-bayseq)
 752        ("r-genomeinfodb" ,r-genomeinfodb)
 753        ("r-genomicranges" ,r-genomicranges)
 754        ("r-iranges" ,r-iranges)
 755        ("r-rsamtools" ,r-rsamtools)
 756        ("r-seqlogo" ,r-seqlogo)))
 757     (home-page "https://bioconductor.org/packages/riboSeqR/")
 758     (synopsis "Analysis of sequencing data from ribosome profiling experiments")
 759     (description
 760      "This package provides plotting functions, frameshift detection and
 761 parsing of genetic sequencing data from ribosome profiling experiments.")
 762     (license license:gpl3)))
 763
 764 (define-public r-interactionset
 765   (package
 766     (name "r-interactionset")
 767     (version "1.10.0")
 768     (source
 769      (origin
 770        (method url-fetch)
 771        (uri (bioconductor-uri "InteractionSet" version))
 772        (sha256
 773         (base32
 774          "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
 775     (properties
 776      `((upstream-name . "InteractionSet")))
 777     (build-system r-build-system)
 778     (propagated-inputs
 779      `(("r-biocgenerics" ,r-biocgenerics)
 780        ("r-genomeinfodb" ,r-genomeinfodb)
 781        ("r-genomicranges" ,r-genomicranges)
 782        ("r-iranges" ,r-iranges)
 783        ("r-matrix" ,r-matrix)
 784        ("r-rcpp" ,r-rcpp)
 785        ("r-s4vectors" ,r-s4vectors)
 786        ("r-summarizedexperiment" ,r-summarizedexperiment)))
 787     (home-page "https://bioconductor.org/packages/InteractionSet")
 788     (synopsis "Base classes for storing genomic interaction data")
 789     (description
 790      "This packages provides the @code{GInteractions},
 791 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
 792 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
 793 experiments.")
 794     (license license:gpl3)))
 795
 796 (define-public r-genomicinteractions
 797   (package
 798     (name "r-genomicinteractions")
 799     (version "1.16.0")
 800     (source
 801      (origin
 802        (method url-fetch)
 803        (uri (bioconductor-uri "GenomicInteractions" version))
 804        (sha256
 805         (base32
 806          "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
 807     (properties
 808      `((upstream-name . "GenomicInteractions")))
 809     (build-system r-build-system)
 810     (propagated-inputs
 811      `(("r-biobase" ,r-biobase)
 812        ("r-biocgenerics" ,r-biocgenerics)
 813        ("r-data-table" ,r-data-table)
 814        ("r-dplyr" ,r-dplyr)
 815        ("r-genomeinfodb" ,r-genomeinfodb)
 816        ("r-genomicranges" ,r-genomicranges)
 817        ("r-ggplot2" ,r-ggplot2)
 818        ("r-gridextra" ,r-gridextra)
 819        ("r-gviz" ,r-gviz)
 820        ("r-igraph" ,r-igraph)
 821        ("r-interactionset" ,r-interactionset)
 822        ("r-iranges" ,r-iranges)
 823        ("r-rsamtools" ,r-rsamtools)
 824        ("r-rtracklayer" ,r-rtracklayer)
 825        ("r-s4vectors" ,r-s4vectors)
 826        ("r-stringr" ,r-stringr)))
 827     (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
 828     (synopsis "R package for handling genomic interaction data")
 829     (description
 830      "This R package provides tools for handling genomic interaction data,
 831 such as ChIA-PET/Hi-C, annotating genomic features with interaction
 832 information and producing various plots and statistics.")
 833     (license license:gpl3)))
 834
 835 (define-public r-ctc
 836   (package
 837     (name "r-ctc")
 838     (version "1.56.0")
 839     (source
 840      (origin
 841        (method url-fetch)
 842        (uri (bioconductor-uri "ctc" version))
 843        (sha256
 844         (base32
 845          "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
 846     (build-system r-build-system)
 847     (propagated-inputs `(("r-amap" ,r-amap)))
 848     (home-page "https://bioconductor.org/packages/ctc/")
 849     (synopsis "Cluster and tree conversion")
 850     (description
 851      "This package provides tools for exporting and importing classification
 852 trees and clusters to other programs.")
 853     (license license:gpl2)))
 854
 855 (define-public r-goseq
 856   (package
 857     (name "r-goseq")
 858     (version "1.34.1")
 859     (source
 860      (origin
 861        (method url-fetch)
 862        (uri (bioconductor-uri "goseq" version))
 863        (sha256
 864         (base32
 865          "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
 866     (build-system r-build-system)
 867     (propagated-inputs
 868      `(("r-annotationdbi" ,r-annotationdbi)
 869        ("r-biasedurn" ,r-biasedurn)
 870        ("r-biocgenerics" ,r-biocgenerics)
 871        ("r-genelendatabase" ,r-genelendatabase)
 872        ("r-go-db" ,r-go-db)
 873        ("r-mgcv" ,r-mgcv)))
 874     (home-page "https://bioconductor.org/packages/goseq/")
 875     (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
 876     (description
 877      "This package provides tools to detect Gene Ontology and/or other user
 878 defined categories which are over/under represented in RNA-seq data.")
 879     (license license:lgpl2.0+)))
 880
 881 (define-public r-glimma
 882   (package
 883     (name "r-glimma")
 884     (version "1.10.1")
 885     (source
 886      (origin
 887        (method url-fetch)
 888        (uri (bioconductor-uri "Glimma" version))
 889        (sha256
 890         (base32
 891          "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
 892     (properties `((upstream-name . "Glimma")))
 893     (build-system r-build-system)
 894     (propagated-inputs
 895      `(("r-edger" ,r-edger)
 896        ("r-jsonlite" ,r-jsonlite)
 897        ("r-s4vectors" ,r-s4vectors)))
 898     (home-page "https://github.com/Shians/Glimma")
 899     (synopsis "Interactive HTML graphics")
 900     (description
 901      "This package generates interactive visualisations for analysis of
 902 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
 903 HTML page.  The interactions are built on top of the popular static
 904 representations of analysis results in order to provide additional
 905 information.")
 906     (license license:lgpl3)))
 907
 908 (define-public r-rots
 909   (package
 910     (name "r-rots")
 911     (version "1.10.1")
 912     (source
 913      (origin
 914        (method url-fetch)
 915        (uri (bioconductor-uri "ROTS" version))
 916        (sha256
 917         (base32
 918          "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
 919     (properties `((upstream-name . "ROTS")))
 920     (build-system r-build-system)
 921     (propagated-inputs
 922      `(("r-biobase" ,r-biobase)
 923        ("r-rcpp" ,r-rcpp)))
 924     (home-page "https://bioconductor.org/packages/ROTS/")
 925     (synopsis "Reproducibility-Optimized Test Statistic")
 926     (description
 927      "This package provides tools for calculating the
 928 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
 929 in omics data.")
 930     (license license:gpl2+)))
 931
 932 (define-public r-plgem
 933   (package
 934     (name "r-plgem")
 935     (version "1.54.1")
 936     (source
 937      (origin
 938        (method url-fetch)
 939        (uri (bioconductor-uri "plgem" version))
 940        (sha256
 941         (base32
 942          "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
 943     (build-system r-build-system)
 944     (propagated-inputs
 945      `(("r-biobase" ,r-biobase)
 946        ("r-mass" ,r-mass)))
 947     (home-page "http://www.genopolis.it")
 948     (synopsis "Detect differential expression in microarray and proteomics datasets")
 949     (description
 950      "The Power Law Global Error Model (PLGEM) has been shown to faithfully
 951 model the variance-versus-mean dependence that exists in a variety of
 952 genome-wide datasets, including microarray and proteomics data.  The use of
 953 PLGEM has been shown to improve the detection of differentially expressed
 954 genes or proteins in these datasets.")
 955     (license license:gpl2)))
 956
 957 (define-public r-inspect
 958   (package
 959     (name "r-inspect")
 960     (version "1.12.1")
 961     (source
 962      (origin
 963        (method url-fetch)
 964        (uri (bioconductor-uri "INSPEcT" version))
 965        (sha256
 966         (base32
 967          "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
 968     (properties `((upstream-name . "INSPEcT")))
 969     (build-system r-build-system)
 970     (propagated-inputs
 971      `(("r-biobase" ,r-biobase)
 972        ("r-biocgenerics" ,r-biocgenerics)
 973        ("r-biocparallel" ,r-biocparallel)
 974        ("r-deseq2" ,r-deseq2)
 975        ("r-desolve" ,r-desolve)
 976        ("r-genomicalignments" ,r-genomicalignments)
 977        ("r-genomicfeatures" ,r-genomicfeatures)
 978        ("r-genomicranges" ,r-genomicranges)
 979        ("r-iranges" ,r-iranges)
 980        ("r-plgem" ,r-plgem)
 981        ("r-preprocesscore" ,r-preprocesscore)
 982        ("r-proc" ,r-proc)
 983        ("r-rootsolve" ,r-rootsolve)
 984        ("r-rsamtools" ,r-rsamtools)
 985        ("r-s4vectors" ,r-s4vectors)
 986        ("r-shiny" ,r-shiny)
 987        ("r-summarizedexperiment" ,r-summarizedexperiment)
 988        ("r-txdb-mmusculus-ucsc-mm9-knowngene"
 989         ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
 990     (home-page "https://bioconductor.org/packages/INSPEcT")
 991     (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
 992     (description
 993      "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
 994 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
 995 order to evaluate synthesis, processing and degradation rates and assess via
 996 modeling the rates that determines changes in mature mRNA levels.")
 997     (license license:gpl2)))
 998
 999 (define-public r-dnabarcodes
1000   (package
1001     (name "r-dnabarcodes")
1002     (version "1.12.0")
1003     (source
1004      (origin
1005        (method url-fetch)
1006        (uri (bioconductor-uri "DNABarcodes" version))
1007        (sha256
1008         (base32
1009          "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
1010     (properties `((upstream-name . "DNABarcodes")))
1011     (build-system r-build-system)
1012     (propagated-inputs
1013      `(("r-bh" ,r-bh)
1014        ("r-matrix" ,r-matrix)
1015        ("r-rcpp" ,r-rcpp)))
1016     (home-page "https://bioconductor.org/packages/DNABarcodes")
1017     (synopsis "Create and analyze DNA barcodes")
1018     (description
1019      "This package offers tools to create DNA barcode sets capable of
1020 correcting insertion, deletion, and substitution errors.  Existing barcodes
1021 can be analyzed regarding their minimal, maximal and average distances between
1022 barcodes.  Finally, reads that start with a (possibly mutated) barcode can be
1023 demultiplexed, i.e. assigned to their original reference barcode.")
1024     (license license:gpl2)))
1025
1026 (define-public r-ruvseq
1027   (package
1028     (name "r-ruvseq")
1029     (version "1.16.1")
1030     (source
1031      (origin
1032        (method url-fetch)
1033        (uri (bioconductor-uri "RUVSeq" version))
1034        (sha256
1035         (base32
1036          "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
1037     (properties `((upstream-name . "RUVSeq")))
1038     (build-system r-build-system)
1039     (propagated-inputs
1040      `(("r-biobase" ,r-biobase)
1041        ("r-edaseq" ,r-edaseq)
1042        ("r-edger" ,r-edger)
1043        ("r-mass" ,r-mass)))
1044     (home-page "https://github.com/drisso/RUVSeq")
1045     (synopsis "Remove unwanted variation from RNA-Seq data")
1046     (description
1047      "This package implements methods to @dfn{remove unwanted variation} (RUV)
1048 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1049 samples.")
1050     (license license:artistic2.0)))
1051
1052 (define-public r-biocneighbors
1053   (package
1054     (name "r-biocneighbors")
1055     (version "1.0.0")
1056     (source
1057      (origin
1058        (method url-fetch)
1059        (uri (bioconductor-uri "BiocNeighbors" version))
1060        (sha256
1061         (base32
1062          "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
1063     (properties `((upstream-name . "BiocNeighbors")))
1064     (build-system r-build-system)
1065     (propagated-inputs
1066      `(("r-biocparallel" ,r-biocparallel)
1067        ("r-rcpp" ,r-rcpp)
1068        ("r-rcppannoy" ,r-rcppannoy)
1069        ("r-s4vectors" ,r-s4vectors)))
1070     (home-page "https://bioconductor.org/packages/BiocNeighbors")
1071     (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1072     (description
1073      "This package implements exact and approximate methods for nearest
1074 neighbor detection, in a framework that allows them to be easily switched
1075 within Bioconductor packages or workflows.  The exact algorithm is implemented
1076 using pre-clustering with the k-means algorithm.  Functions are also provided
1077 to search for all neighbors within a given distance.  Parallelization is
1078 achieved for all methods using the BiocParallel framework.")
1079     (license license:gpl3)))
1080
1081 (define-public r-destiny
1082   (package
1083     (name "r-destiny")
1084     (version "2.12.0")
1085     (source
1086      (origin
1087        (method url-fetch)
1088        (uri (bioconductor-uri "destiny" version))
1089        (sha256
1090         (base32
1091          "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
1092     (build-system r-build-system)
1093     (propagated-inputs
1094      `(("r-biobase" ,r-biobase)
1095        ("r-biocgenerics" ,r-biocgenerics)
1096        ("r-fnn" ,r-fnn)
1097        ("r-ggthemes" ,r-ggthemes)
1098        ("r-hmisc" ,r-hmisc)
1099        ("r-igraph" ,r-igraph)
1100        ("r-matrix" ,r-matrix)
1101        ("r-proxy" ,r-proxy)
1102        ("r-rcpp" ,r-rcpp)
1103        ("r-rcppeigen" ,r-rcppeigen)
1104        ("r-scales" ,r-scales)
1105        ("r-scatterplot3d" ,r-scatterplot3d)
1106        ("r-smoother" ,r-smoother)
1107        ("r-summarizedexperiment" ,r-summarizedexperiment)
1108        ("r-vim" ,r-vim)))
1109     (home-page "https://bioconductor.org/packages/destiny/")
1110     (synopsis "Create and plot diffusion maps")
1111     (description "This package provides tools to create and plot diffusion
1112 maps.")
1113     ;; Any version of the GPL
1114     (license license:gpl3+)))
1115
1116 (define-public r-savr
1117   (package
1118     (name "r-savr")
1119     (version "1.20.0")
1120     (source
1121      (origin
1122        (method url-fetch)
1123        (uri (bioconductor-uri "savR" version))
1124        (sha256
1125         (base32
1126          "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
1127     (properties `((upstream-name . "savR")))
1128     (build-system r-build-system)
1129     (propagated-inputs
1130      `(("r-ggplot2" ,r-ggplot2)
1131        ("r-gridextra" ,r-gridextra)
1132        ("r-reshape2" ,r-reshape2)
1133        ("r-scales" ,r-scales)
1134        ("r-xml" ,r-xml)))
1135     (home-page "https://github.com/bcalder/savR")
1136     (synopsis "Parse and analyze Illumina SAV files")
1137     (description
1138      "This package provides tools to parse Illumina Sequence Analysis
1139 Viewer (SAV) files, access data, and generate QC plots.")
1140     (license license:agpl3+)))
1141
1142 (define-public r-chipexoqual
1143   (package
1144     (name "r-chipexoqual")
1145     (version "1.6.0")
1146     (source
1147      (origin
1148        (method url-fetch)
1149        (uri (bioconductor-uri "ChIPexoQual" version))
1150        (sha256
1151         (base32
1152          "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
1153     (properties `((upstream-name . "ChIPexoQual")))
1154     (build-system r-build-system)
1155     (propagated-inputs
1156      `(("r-biocparallel" ,r-biocparallel)
1157        ("r-biovizbase" ,r-biovizbase)
1158        ("r-broom" ,r-broom)
1159        ("r-data-table" ,r-data-table)
1160        ("r-dplyr" ,r-dplyr)
1161        ("r-genomeinfodb" ,r-genomeinfodb)
1162        ("r-genomicalignments" ,r-genomicalignments)
1163        ("r-genomicranges" ,r-genomicranges)
1164        ("r-ggplot2" ,r-ggplot2)
1165        ("r-hexbin" ,r-hexbin)
1166        ("r-iranges" ,r-iranges)
1167        ("r-rcolorbrewer" ,r-rcolorbrewer)
1168        ("r-rmarkdown" ,r-rmarkdown)
1169        ("r-rsamtools" ,r-rsamtools)
1170        ("r-s4vectors" ,r-s4vectors)
1171        ("r-scales" ,r-scales)
1172        ("r-viridis" ,r-viridis)))
1173     (home-page "https://github.com/keleslab/ChIPexoQual")
1174     (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1175     (description
1176      "This package provides a quality control pipeline for ChIP-exo/nexus
1177 sequencing data.")
1178     (license license:gpl2+)))