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 gcc)
  31   #:use-module (gnu packages graph)
  32   #:use-module (gnu packages maths)
  33   #:use-module (gnu packages statistics)
  34   #:use-module (gnu packages web))
  35
  36 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
  37   (package
  38     (name "r-bsgenome-dmelanogaster-ucsc-dm6")
  39     (version "1.4.1")
  40     (source (origin
  41               (method url-fetch)
  42               ;; We cannot use bioconductor-uri here because this tarball is
  43               ;; located under "data/annotation/" instead of "bioc/".
  44               (uri (string-append "https://www.bioconductor.org/packages/"
  45                                   "release/data/annotation/src/contrib/"
  46                                   "BSgenome.Dmelanogaster.UCSC.dm6_"
  47                                   version ".tar.gz"))
  48               (sha256
  49                (base32
  50                 "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
  51     (properties
  52      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
  53     (build-system r-build-system)
  54     ;; As this package provides little more than a very large data file it
  55     ;; doesn't make sense to build substitutes.
  56     (arguments `(#:substitutable? #f))
  57     (propagated-inputs
  58      `(("r-bsgenome" ,r-bsgenome)))
  59     (home-page
  60      "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
  61     (synopsis "Full genome sequences for Fly")
  62     (description
  63      "This package provides full genome sequences for Drosophila
  64 melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
  65 objects.")
  66     (license license:artistic2.0)))
  67
  68 (define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
  69   (package
  70     (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
  71     (version "1.3.99")
  72     (source (origin
  73               (method url-fetch)
  74               ;; We cannot use bioconductor-uri here because this tarball is
  75               ;; located under "data/annotation/" instead of "bioc/".
  76               (uri (string-append "http://www.bioconductor.org/packages/"
  77                                   "release/data/annotation/src/contrib/"
  78                                   "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
  79                                   version ".tar.gz"))
  80               (sha256
  81                (base32
  82                 "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
  83     (properties
  84      `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
  85     (build-system r-build-system)
  86     (propagated-inputs
  87      `(("r-bsgenome" ,r-bsgenome)
  88        ("r-bsgenome-dmelanogaster-ucsc-dm3"
  89         ,r-bsgenome-dmelanogaster-ucsc-dm3)))
  90     (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
  91     (synopsis "Full masked genome sequences for Fly")
  92     (description
  93      "This package provides full masked genome sequences for Drosophila
  94 melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
  95 Biostrings objects.  The sequences are the same as in
  96 BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
  97 masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
  98 intra-contig ambiguities (AMB mask), (3) the mask of repeats from
  99 RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
 100 Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
 101     (license license:artistic2.0)))
 102
 103 (define-public r-bsgenome-hsapiens-ucsc-hg19-masked
 104   (package
 105     (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
 106     (version "1.3.99")
 107     (source (origin
 108               (method url-fetch)
 109               ;; We cannot use bioconductor-uri here because this tarball is
 110               ;; located under "data/annotation/" instead of "bioc/".
 111               (uri (string-append "http://www.bioconductor.org/packages/"
 112                                   "release/data/annotation/src/contrib/"
 113                                   "BSgenome.Hsapiens.UCSC.hg19.masked_"
 114                                   version ".tar.gz"))
 115               (sha256
 116                (base32
 117                 "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
 118     (properties
 119      `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
 120     (build-system r-build-system)
 121     (propagated-inputs
 122      `(("r-bsgenome" ,r-bsgenome)
 123        ("r-bsgenome-hsapiens-ucsc-hg19"
 124         ,r-bsgenome-hsapiens-ucsc-hg19)))
 125     (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
 126     (synopsis "Full masked genome sequences for Homo sapiens")
 127     (description
 128      "This package provides full genome sequences for Homo sapiens (Human) as
 129 provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.  The
 130 sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
 131 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
 132 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
 133 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
 134 Repeats Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by
 135 default.")
 136     (license license:artistic2.0)))
 137
 138 (define-public r-bsgenome-mmusculus-ucsc-mm9-masked
 139   (package
 140     (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
 141     (version "1.3.99")
 142     (source (origin
 143               (method url-fetch)
 144               ;; We cannot use bioconductor-uri here because this tarball is
 145               ;; located under "data/annotation/" instead of "bioc/".
 146               (uri (string-append "http://www.bioconductor.org/packages/"
 147                                   "release/data/annotation/src/contrib/"
 148                                   "BSgenome.Mmusculus.UCSC.mm9.masked_"
 149                                   version ".tar.gz"))
 150               (sha256
 151                (base32
 152                 "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
 153     (properties
 154      `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
 155     (build-system r-build-system)
 156     (propagated-inputs
 157      `(("r-bsgenome" ,r-bsgenome)
 158        ("r-bsgenome-mmusculus-ucsc-mm9"
 159         ,r-bsgenome-mmusculus-ucsc-mm9)))
 160     (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
 161     (synopsis "Full masked genome sequences for Mouse")
 162     (description
 163      "This package provides full genome sequences for Mus musculus (Mouse) as
 164 provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.  The
 165 sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
 166 them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
 167 mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
 168 repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
 169 Repeats Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by
 170 default."  )
 171     (license license:artistic2.0)))
 172
 173 (define-public r-genelendatabase
 174   (package
 175     (name "r-genelendatabase")
 176     (version "1.16.0")
 177     (source
 178      (origin
 179        (method url-fetch)
 180        ;; We cannot use bioconductor-uri here because this tarball is
 181        ;; located under "data/experiment/" instead of "bioc/".
 182        (uri (string-append "https://bioconductor.org/packages/"
 183                            "release/data/experiment/src/contrib"
 184                            "/geneLenDataBase_" version ".tar.gz"))
 185        (sha256
 186         (base32
 187          "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
 188     (properties
 189      `((upstream-name . "geneLenDataBase")))
 190     (build-system r-build-system)
 191     (propagated-inputs
 192      `(("r-rtracklayer" ,r-rtracklayer)
 193        ("r-genomicfeatures" ,r-genomicfeatures)))
 194     (home-page "https://bioconductor.org/packages/geneLenDataBase/")
 195     (synopsis "Lengths of mRNA transcripts for a number of genomes")
 196     (description
 197      "This package provides the lengths of mRNA transcripts for a number of
 198 genomes and gene ID formats, largely based on the UCSC table browser.")
 199     (license license:lgpl2.0+)))
 200
 201 (define-public r-txdb-mmusculus-ucsc-mm9-knowngene
 202   (package
 203     (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
 204     (version "3.2.2")
 205     (source (origin
 206               (method url-fetch)
 207               ;; We cannot use bioconductor-uri here because this tarball is
 208               ;; located under "data/annotation/" instead of "bioc/".
 209               (uri (string-append "https://bioconductor.org/packages/"
 210                                   "release/data/annotation/src/contrib"
 211                                   "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
 212                                   version ".tar.gz"))
 213               (sha256
 214                (base32
 215                 "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
 216     (properties
 217      `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
 218     (build-system r-build-system)
 219     (propagated-inputs
 220      `(("r-genomicfeatures" ,r-genomicfeatures)
 221        ("r-annotationdbi" ,r-annotationdbi)))
 222     (home-page
 223      "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
 224     (synopsis "Annotation package for mouse genome in TxDb format")
 225     (description
 226      "This package provides an annotation database of Mouse genome data.  It
 227 is derived from the UCSC mm9 genome and based on the \"knownGene\" track.  The
 228 database is exposed as a @code{TxDb} object.")
 229     (license license:artistic2.0)))
 230
 231 \f
 232 (define-public r-biocgenerics
 233   (package
 234     (name "r-biocgenerics")
 235     (version "0.28.0")
 236     (source (origin
 237               (method url-fetch)
 238               (uri (bioconductor-uri "BiocGenerics" version))
 239               (sha256
 240                (base32
 241                 "0cvpsrhg7sn7lpqgxvqrsagv6j7xj5rafq5xdjfd8zc4gxrs5rb8"))))
 242     (properties
 243      `((upstream-name . "BiocGenerics")))
 244     (build-system r-build-system)
 245     (home-page "https://bioconductor.org/packages/BiocGenerics")
 246     (synopsis "S4 generic functions for Bioconductor")
 247     (description
 248      "This package provides S4 generic functions needed by many Bioconductor
 249 packages.")
 250     (license license:artistic2.0)))
 251
 252 (define-public r-annotate
 253   (package
 254     (name "r-annotate")
 255     (version "1.60.0")
 256     (source
 257      (origin
 258        (method url-fetch)
 259        (uri (bioconductor-uri "annotate" version))
 260        (sha256
 261         (base32
 262          "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
 263     (build-system r-build-system)
 264     (propagated-inputs
 265      `(("r-annotationdbi" ,r-annotationdbi)
 266        ("r-biobase" ,r-biobase)
 267        ("r-biocgenerics" ,r-biocgenerics)
 268        ("r-dbi" ,r-dbi)
 269        ("r-rcurl" ,r-rcurl)
 270        ("r-xml" ,r-xml)
 271        ("r-xtable" ,r-xtable)))
 272     (home-page
 273      "https://bioconductor.org/packages/annotate")
 274     (synopsis "Annotation for microarrays")
 275     (description "This package provides R environments for the annotation of
 276 microarrays.")
 277     (license license:artistic2.0)))
 278
 279 (define-public r-hpar
 280   (package
 281     (name "r-hpar")
 282     (version "1.24.0")
 283     (source
 284      (origin
 285        (method url-fetch)
 286        (uri (bioconductor-uri "hpar" version))
 287        (sha256
 288         (base32
 289          "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
 290     (build-system r-build-system)
 291     (home-page "https://bioconductor.org/packages/hpar/")
 292     (synopsis "Human Protein Atlas in R")
 293     (description "This package provides a simple interface to and data from
 294 the Human Protein Atlas project.")
 295     (license license:artistic2.0)))
 296
 297 (define-public r-regioner
 298   (package
 299     (name "r-regioner")
 300     (version "1.14.0")
 301     (source
 302      (origin
 303        (method url-fetch)
 304        (uri (bioconductor-uri "regioneR" version))
 305        (sha256
 306         (base32
 307          "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
 308     (properties `((upstream-name . "regioneR")))
 309     (build-system r-build-system)
 310     (propagated-inputs
 311      `(("r-biostrings" ,r-biostrings)
 312        ("r-bsgenome" ,r-bsgenome)
 313        ("r-genomeinfodb" ,r-genomeinfodb)
 314        ("r-genomicranges" ,r-genomicranges)
 315        ("r-iranges" ,r-iranges)
 316        ("r-memoise" ,r-memoise)
 317        ("r-rtracklayer" ,r-rtracklayer)
 318        ("r-s4vectors" ,r-s4vectors)))
 319     (home-page "https://bioconductor.org/packages/regioneR/")
 320     (synopsis "Association analysis of genomic regions")
 321     (description "This package offers a statistical framework based on
 322 customizable permutation tests to assess the association between genomic
 323 region sets and other genomic features.")
 324     (license license:artistic2.0)))
 325
 326 (define-public r-diffbind
 327   (package
 328     (name "r-diffbind")
 329     (version "2.10.0")
 330     (source
 331      (origin
 332        (method url-fetch)
 333        (uri (bioconductor-uri "DiffBind" version))
 334        (sha256
 335         (base32
 336          "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
 337     (properties `((upstream-name . "DiffBind")))
 338     (build-system r-build-system)
 339     (inputs
 340      `(("zlib" ,zlib)))
 341     (propagated-inputs
 342      `(("r-amap" ,r-amap)
 343        ("r-biocparallel" ,r-biocparallel)
 344        ("r-deseq2" ,r-deseq2)
 345        ("r-dplyr" ,r-dplyr)
 346        ("r-edger" ,r-edger)
 347        ("r-genomicalignments" ,r-genomicalignments)
 348        ("r-genomicranges" ,r-genomicranges)
 349        ("r-ggplot2" ,r-ggplot2)
 350        ("r-ggrepel" ,r-ggrepel)
 351        ("r-gplots" ,r-gplots)
 352        ("r-iranges" ,r-iranges)
 353        ("r-lattice" ,r-lattice)
 354        ("r-limma" ,r-limma)
 355        ("r-locfit" ,r-locfit)
 356        ("r-rcolorbrewer" , r-rcolorbrewer)
 357        ("r-rcpp" ,r-rcpp)
 358        ("r-rsamtools" ,r-rsamtools)
 359        ("r-s4vectors" ,r-s4vectors)
 360        ("r-summarizedexperiment" ,r-summarizedexperiment)
 361        ("r-systempiper" ,r-systempiper)
 362        ("r-zlibbioc" ,r-zlibbioc)))
 363     (home-page "http://bioconductor.org/packages/DiffBind")
 364     (synopsis "Differential binding analysis of ChIP-Seq peak data")
 365     (description
 366      "This package computes differentially bound sites from multiple
 367 ChIP-seq experiments using affinity (quantitative) data.  Also enables
 368 occupancy (overlap) analysis and plotting functions.")
 369     (license license:artistic2.0)))
 370
 371 (define-public r-ripseeker
 372   (package
 373     (name "r-ripseeker")
 374     (version "1.22.0")
 375     (source
 376      (origin
 377        (method url-fetch)
 378        (uri (bioconductor-uri "RIPSeeker" version))
 379        (sha256
 380         (base32
 381          "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
 382     (properties `((upstream-name . "RIPSeeker")))
 383     (build-system r-build-system)
 384     (propagated-inputs
 385      `(("r-s4vectors" ,r-s4vectors)
 386        ("r-iranges" ,r-iranges)
 387        ("r-genomicranges" ,r-genomicranges)
 388        ("r-summarizedexperiment" ,r-summarizedexperiment)
 389        ("r-rsamtools" ,r-rsamtools)
 390        ("r-genomicalignments" ,r-genomicalignments)
 391        ("r-rtracklayer" ,r-rtracklayer)))
 392     (home-page "http://bioconductor.org/packages/RIPSeeker")
 393     (synopsis
 394      "Identifying protein-associated transcripts from RIP-seq experiments")
 395     (description
 396      "This package infers and discriminates RIP peaks from RIP-seq alignments
 397 using two-state HMM with negative binomial emission probability.  While
 398 RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
 399 a suite of bioinformatics tools integrated within this self-contained software
 400 package comprehensively addressing issues ranging from post-alignments
 401 processing to visualization and annotation.")
 402     (license license:gpl2)))
 403
 404 (define-public r-multtest
 405   (package
 406     (name "r-multtest")
 407     (version "2.38.0")
 408     (source
 409      (origin
 410        (method url-fetch)
 411        (uri (bioconductor-uri "multtest" version))
 412        (sha256
 413         (base32
 414          "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
 415     (build-system r-build-system)
 416     (propagated-inputs
 417      `(("r-survival" ,r-survival)
 418        ("r-biocgenerics" ,r-biocgenerics)
 419        ("r-biobase" ,r-biobase)
 420        ("r-mass" ,r-mass)))
 421     (home-page "http://bioconductor.org/packages/multtest")
 422     (synopsis "Resampling-based multiple hypothesis testing")
 423     (description
 424      "This package can do non-parametric bootstrap and permutation
 425 resampling-based multiple testing procedures (including empirical Bayes
 426 methods) for controlling the family-wise error rate (FWER), generalized
 427 family-wise error rate (gFWER), tail probability of the proportion of
 428 false positives (TPPFP), and false discovery rate (FDR).  Several choices
 429 of bootstrap-based null distribution are implemented (centered, centered
 430 and scaled, quantile-transformed).  Single-step and step-wise methods are
 431 available.  Tests based on a variety of T- and F-statistics (including
 432 T-statistics based on regression parameters from linear and survival models
 433 as well as those based on correlation parameters) are included.  When probing
 434 hypotheses with T-statistics, users may also select a potentially faster null
 435 distribution which is multivariate normal with mean zero and variance
 436 covariance matrix derived from the vector influence function.  Results are
 437 reported in terms of adjusted P-values, confidence regions and test statistic
 438 cutoffs.  The procedures are directly applicable to identifying differentially
 439 expressed genes in DNA microarray experiments.")
 440     (license license:lgpl3)))
 441
 442 (define-public r-graph
 443   (package
 444     (name "r-graph")
 445     (version "1.60.0")
 446     (source (origin
 447               (method url-fetch)
 448               (uri (bioconductor-uri "graph" version))
 449               (sha256
 450                (base32
 451                 "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
 452     (build-system r-build-system)
 453     (propagated-inputs
 454      `(("r-biocgenerics" ,r-biocgenerics)))
 455     (home-page "https://bioconductor.org/packages/graph")
 456     (synopsis "Handle graph data structures in R")
 457     (description
 458      "This package implements some simple graph handling capabilities for R.")
 459     (license license:artistic2.0)))
 460
 461 (define-public r-codedepends
 462   (package
 463     (name "r-codedepends")
 464     (version "0.6.5")
 465     (source
 466      (origin
 467        (method url-fetch)
 468        (uri (cran-uri "CodeDepends" version))
 469        (sha256
 470         (base32
 471          "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
 472     (properties `((upstream-name . "CodeDepends")))
 473     (build-system r-build-system)
 474     (propagated-inputs
 475      `(("r-codetools" ,r-codetools)
 476        ("r-graph" ,r-graph)
 477        ("r-xml" ,r-xml)))
 478     (home-page "http://cran.r-project.org/web/packages/CodeDepends")
 479     (synopsis "Analysis of R code for reproducible research and code comprehension")
 480     (description
 481      "This package provides tools for analyzing R expressions or blocks of
 482 code and determining the dependencies between them.  It focuses on R scripts,
 483 but can be used on the bodies of functions.  There are many facilities
 484 including the ability to summarize or get a high-level view of code,
 485 determining dependencies between variables, code improvement suggestions.")
 486     ;; Any version of the GPL
 487     (license (list license:gpl2+ license:gpl3+))))
 488
 489 (define-public r-chippeakanno
 490   (package
 491     (name "r-chippeakanno")
 492     (version "3.16.1")
 493     (source
 494      (origin
 495        (method url-fetch)
 496        (uri (bioconductor-uri "ChIPpeakAnno" version))
 497        (sha256
 498         (base32
 499          "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
 500     (properties `((upstream-name . "ChIPpeakAnno")))
 501     (build-system r-build-system)
 502     (propagated-inputs
 503      `(("r-biocgenerics" ,r-biocgenerics)
 504        ("r-biocmanager" ,r-biocmanager)
 505        ("r-biostrings" ,r-biostrings)
 506        ("r-delayedarray" ,r-delayedarray)
 507        ("r-go-db" ,r-go-db)
 508        ("r-biomart" ,r-biomart)
 509        ("r-bsgenome" ,r-bsgenome)
 510        ("r-genomicfeatures" ,r-genomicfeatures)
 511        ("r-genomicranges" ,r-genomicranges)
 512        ("r-genomeinfodb" ,r-genomeinfodb)
 513        ("r-iranges" ,r-iranges)
 514        ("r-matrixstats" ,r-matrixstats)
 515        ("r-annotationdbi" ,r-annotationdbi)
 516        ("r-limma" ,r-limma)
 517        ("r-multtest" ,r-multtest)
 518        ("r-rbgl" ,r-rbgl)
 519        ("r-graph" ,r-graph)
 520        ("r-regioner" ,r-regioner)
 521        ("r-dbi" ,r-dbi)
 522        ("r-ensembldb" ,r-ensembldb)
 523        ("r-biobase" ,r-biobase)
 524        ("r-s4vectors" ,r-s4vectors)
 525        ("r-seqinr" ,r-seqinr)
 526        ("r-idr" ,r-idr)
 527        ("r-genomicalignments" ,r-genomicalignments)
 528        ("r-summarizedexperiment" ,r-summarizedexperiment)
 529        ("r-rsamtools" ,r-rsamtools)
 530        ("r-venndiagram" ,r-venndiagram)))
 531     (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
 532     (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
 533     (description
 534      "The package includes functions to retrieve the sequences around the peak,
 535 obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
 536 custom features such as most conserved elements and other transcription factor
 537 binding sites supplied by users.  Starting 2.0.5, new functions have been added
 538 for finding the peaks with bi-directional promoters with summary statistics
 539 (peaksNearBDP), for summarizing the occurrence of motifs in peaks
 540 (summarizePatternInPeaks) and for adding other IDs to annotated peaks or
 541 enrichedGO (addGeneIDs).")
 542     (license license:gpl2+)))
 543
 544 (define-public r-marray
 545   (package
 546     (name "r-marray")
 547     (version "1.60.0")
 548     (source (origin
 549               (method url-fetch)
 550               (uri (bioconductor-uri "marray" version))
 551               (sha256
 552                (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
 553     (build-system r-build-system)
 554     (propagated-inputs
 555      `(("r-limma" ,r-limma)))
 556     (home-page "http://bioconductor.org/packages/marray")
 557     (synopsis "Exploratory analysis for two-color spotted microarray data")
 558     (description "This package contains class definitions for two-color spotted
 559 microarray data.  It also includes fuctions for data input, diagnostic plots,
 560 normalization and quality checking.")
 561     (license license:lgpl2.0+)))
 562
 563 (define-public r-cghbase
 564   (package
 565    (name "r-cghbase")
 566    (version "1.42.0")
 567    (source (origin
 568             (method url-fetch)
 569             (uri (bioconductor-uri "CGHbase" version))
 570             (sha256
 571              (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
 572    (properties `((upstream-name . "CGHbase")))
 573    (build-system r-build-system)
 574    (propagated-inputs
 575     `(("r-biobase" ,r-biobase)
 576       ("r-marray" ,r-marray)))
 577    (home-page "http://bioconductor.org/packages/CGHbase")
 578    (synopsis "Base functions and classes for arrayCGH data analysis")
 579    (description "This package contains functions and classes that are needed by
 580 the @code{arrayCGH} packages.")
 581    (license license:gpl2+)))
 582
 583 (define-public r-cghcall
 584   (package
 585    (name "r-cghcall")
 586    (version "2.44.0")
 587    (source (origin
 588             (method url-fetch)
 589             (uri (bioconductor-uri "CGHcall" version))
 590             (sha256
 591              (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
 592    (properties `((upstream-name . "CGHcall")))
 593    (build-system r-build-system)
 594    (propagated-inputs
 595     `(("r-biobase" ,r-biobase)
 596       ("r-cghbase" ,r-cghbase)
 597       ("r-impute" ,r-impute)
 598       ("r-dnacopy" ,r-dnacopy)
 599       ("r-snowfall" ,r-snowfall)))
 600    (home-page "http://bioconductor.org/packages/CGHcall")
 601    (synopsis "Base functions and classes for arrayCGH data analysis")
 602    (description "This package contains functions and classes that are needed by
 603 @code{arrayCGH} packages.")
 604    (license license:gpl2+)))
 605
 606 (define-public r-qdnaseq
 607   (package
 608     (name "r-qdnaseq")
 609     (version "1.18.0")
 610     (source (origin
 611               (method url-fetch)
 612               (uri (bioconductor-uri "QDNAseq" version))
 613               (sha256
 614                (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
 615     (properties `((upstream-name . "QDNAseq")))
 616     (build-system r-build-system)
 617     (propagated-inputs
 618      `(("r-biobase" ,r-biobase)
 619        ("r-biocparallel" ,r-biocparallel)
 620        ("r-cghbase" ,r-cghbase)
 621        ("r-cghcall" ,r-cghcall)
 622        ("r-dnacopy" ,r-dnacopy)
 623        ("r-genomicranges" ,r-genomicranges)
 624        ("r-iranges" ,r-iranges)
 625        ("r-matrixstats" ,r-matrixstats)
 626        ("r-r-utils" ,r-r-utils)
 627        ("r-rsamtools" ,r-rsamtools)))
 628     (home-page "http://bioconductor.org/packages/QDNAseq")
 629     (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
 630     (description "The genome is divided into non-overlapping fixed-sized bins,
 631 number of sequence reads in each counted, adjusted with a simultaneous
 632 two-dimensional loess correction for sequence mappability and GC content, and
 633 filtered to remove spurious regions in the genome.  Downstream steps of
 634 segmentation and calling are also implemented via packages DNAcopy and CGHcall,
 635 respectively.")
 636     (license license:gpl2+)))
 637
 638 (define-public r-bayseq
 639   (package
 640     (name "r-bayseq")
 641     (version "2.16.0")
 642     (source
 643      (origin
 644        (method url-fetch)
 645        (uri (bioconductor-uri "baySeq" version))
 646        (sha256
 647         (base32
 648          "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
 649     (properties `((upstream-name . "baySeq")))
 650     (build-system r-build-system)
 651     (propagated-inputs
 652      `(("r-abind" ,r-abind)
 653        ("r-edger" ,r-edger)
 654        ("r-genomicranges" ,r-genomicranges)))
 655     (home-page "https://bioconductor.org/packages/baySeq/")
 656     (synopsis "Bayesian analysis of differential expression patterns in count data")
 657     (description
 658      "This package identifies differential expression in high-throughput count
 659 data, such as that derived from next-generation sequencing machines,
 660 calculating estimated posterior likelihoods of differential expression (or
 661 more complex hypotheses) via empirical Bayesian methods.")
 662     (license license:gpl3)))
 663
 664 (define-public r-chipcomp
 665   (package
 666     (name "r-chipcomp")
 667     (version "1.12.0")
 668     (source
 669      (origin
 670        (method url-fetch)
 671        (uri (bioconductor-uri "ChIPComp" version))
 672        (sha256
 673         (base32
 674          "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
 675     (properties `((upstream-name . "ChIPComp")))
 676     (build-system r-build-system)
 677     (propagated-inputs
 678      `(("r-biocgenerics" ,r-biocgenerics)
 679        ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
 680        ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
 681        ("r-genomeinfodb" ,r-genomeinfodb)
 682        ("r-genomicranges" ,r-genomicranges)
 683        ("r-iranges" ,r-iranges)
 684        ("r-limma" ,r-limma)
 685        ("r-rsamtools" ,r-rsamtools)
 686        ("r-rtracklayer" ,r-rtracklayer)
 687        ("r-s4vectors" ,r-s4vectors)))
 688     (home-page "https://bioconductor.org/packages/ChIPComp")
 689     (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
 690     (description
 691      "ChIPComp implements a statistical method for quantitative comparison of
 692 multiple ChIP-seq datasets.  It detects differentially bound sharp binding
 693 sites across multiple conditions considering matching control in ChIP-seq
 694 datasets.")
 695     ;; Any version of the GPL.
 696     (license license:gpl3+)))
 697
 698 (define-public r-riboprofiling
 699   (package
 700     (name "r-riboprofiling")
 701     (version "1.12.0")
 702     (source
 703      (origin
 704        (method url-fetch)
 705        (uri (bioconductor-uri "RiboProfiling" version))
 706        (sha256
 707         (base32
 708          "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
 709     (properties `((upstream-name . "RiboProfiling")))
 710     (build-system r-build-system)
 711     (propagated-inputs
 712      `(("r-biocgenerics" ,r-biocgenerics)
 713        ("r-biostrings" ,r-biostrings)
 714        ("r-data-table" ,r-data-table)
 715        ("r-genomeinfodb" ,r-genomeinfodb)
 716        ("r-genomicalignments" ,r-genomicalignments)
 717        ("r-genomicfeatures" ,r-genomicfeatures)
 718        ("r-genomicranges" ,r-genomicranges)
 719        ("r-ggbio" ,r-ggbio)
 720        ("r-ggplot2" ,r-ggplot2)
 721        ("r-iranges" ,r-iranges)
 722        ("r-plyr" ,r-plyr)
 723        ("r-reshape2" ,r-reshape2)
 724        ("r-rsamtools" ,r-rsamtools)
 725        ("r-rtracklayer" ,r-rtracklayer)
 726        ("r-s4vectors" ,r-s4vectors)
 727        ("r-sqldf" ,r-sqldf)))
 728     (home-page "https://bioconductor.org/packages/RiboProfiling/")
 729     (synopsis "Ribosome profiling data analysis")
 730     (description "Starting with a BAM file, this package provides the
 731 necessary functions for quality assessment, read start position recalibration,
 732 the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
 733 of count data: pairs, log fold-change, codon frequency and coverage
 734 assessment, principal component analysis on codon coverage.")
 735     (license license:gpl3)))
 736
 737 (define-public r-riboseqr
 738   (package
 739     (name "r-riboseqr")
 740     (version "1.16.0")
 741     (source
 742      (origin
 743        (method url-fetch)
 744        (uri (bioconductor-uri "riboSeqR" version))
 745        (sha256
 746         (base32
 747          "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
 748     (properties `((upstream-name . "riboSeqR")))
 749     (build-system r-build-system)
 750     (propagated-inputs
 751      `(("r-abind" ,r-abind)
 752        ("r-bayseq" ,r-bayseq)
 753        ("r-genomeinfodb" ,r-genomeinfodb)
 754        ("r-genomicranges" ,r-genomicranges)
 755        ("r-iranges" ,r-iranges)
 756        ("r-rsamtools" ,r-rsamtools)
 757        ("r-seqlogo" ,r-seqlogo)))
 758     (home-page "https://bioconductor.org/packages/riboSeqR/")
 759     (synopsis "Analysis of sequencing data from ribosome profiling experiments")
 760     (description
 761      "This package provides plotting functions, frameshift detection and
 762 parsing of genetic sequencing data from ribosome profiling experiments.")
 763     (license license:gpl3)))
 764
 765 (define-public r-interactionset
 766   (package
 767     (name "r-interactionset")
 768     (version "1.10.0")
 769     (source
 770      (origin
 771        (method url-fetch)
 772        (uri (bioconductor-uri "InteractionSet" version))
 773        (sha256
 774         (base32
 775          "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
 776     (properties
 777      `((upstream-name . "InteractionSet")))
 778     (build-system r-build-system)
 779     (propagated-inputs
 780      `(("r-biocgenerics" ,r-biocgenerics)
 781        ("r-genomeinfodb" ,r-genomeinfodb)
 782        ("r-genomicranges" ,r-genomicranges)
 783        ("r-iranges" ,r-iranges)
 784        ("r-matrix" ,r-matrix)
 785        ("r-rcpp" ,r-rcpp)
 786        ("r-s4vectors" ,r-s4vectors)
 787        ("r-summarizedexperiment" ,r-summarizedexperiment)))
 788     (home-page "https://bioconductor.org/packages/InteractionSet")
 789     (synopsis "Base classes for storing genomic interaction data")
 790     (description
 791      "This packages provides the @code{GInteractions},
 792 @code{InteractionSet} and @code{ContactMatrix} objects and associated methods
 793 for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
 794 experiments.")
 795     (license license:gpl3)))
 796
 797 (define-public r-genomicinteractions
 798   (package
 799     (name "r-genomicinteractions")
 800     (version "1.16.0")
 801     (source
 802      (origin
 803        (method url-fetch)
 804        (uri (bioconductor-uri "GenomicInteractions" version))
 805        (sha256
 806         (base32
 807          "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
 808     (properties
 809      `((upstream-name . "GenomicInteractions")))
 810     (build-system r-build-system)
 811     (propagated-inputs
 812      `(("r-biobase" ,r-biobase)
 813        ("r-biocgenerics" ,r-biocgenerics)
 814        ("r-data-table" ,r-data-table)
 815        ("r-dplyr" ,r-dplyr)
 816        ("r-genomeinfodb" ,r-genomeinfodb)
 817        ("r-genomicranges" ,r-genomicranges)
 818        ("r-ggplot2" ,r-ggplot2)
 819        ("r-gridextra" ,r-gridextra)
 820        ("r-gviz" ,r-gviz)
 821        ("r-igraph" ,r-igraph)
 822        ("r-interactionset" ,r-interactionset)
 823        ("r-iranges" ,r-iranges)
 824        ("r-rsamtools" ,r-rsamtools)
 825        ("r-rtracklayer" ,r-rtracklayer)
 826        ("r-s4vectors" ,r-s4vectors)
 827        ("r-stringr" ,r-stringr)))
 828     (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
 829     (synopsis "R package for handling genomic interaction data")
 830     (description
 831      "This R package provides tools for handling genomic interaction data,
 832 such as ChIA-PET/Hi-C, annotating genomic features with interaction
 833 information and producing various plots and statistics.")
 834     (license license:gpl3)))
 835
 836 (define-public r-ctc
 837   (package
 838     (name "r-ctc")
 839     (version "1.56.0")
 840     (source
 841      (origin
 842        (method url-fetch)
 843        (uri (bioconductor-uri "ctc" version))
 844        (sha256
 845         (base32
 846          "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
 847     (build-system r-build-system)
 848     (propagated-inputs `(("r-amap" ,r-amap)))
 849     (home-page "https://bioconductor.org/packages/ctc/")
 850     (synopsis "Cluster and tree conversion")
 851     (description
 852      "This package provides tools for exporting and importing classification
 853 trees and clusters to other programs.")
 854     (license license:gpl2)))
 855
 856 (define-public r-goseq
 857   (package
 858     (name "r-goseq")
 859     (version "1.34.1")
 860     (source
 861      (origin
 862        (method url-fetch)
 863        (uri (bioconductor-uri "goseq" version))
 864        (sha256
 865         (base32
 866          "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
 867     (build-system r-build-system)
 868     (propagated-inputs
 869      `(("r-annotationdbi" ,r-annotationdbi)
 870        ("r-biasedurn" ,r-biasedurn)
 871        ("r-biocgenerics" ,r-biocgenerics)
 872        ("r-genelendatabase" ,r-genelendatabase)
 873        ("r-go-db" ,r-go-db)
 874        ("r-mgcv" ,r-mgcv)))
 875     (home-page "https://bioconductor.org/packages/goseq/")
 876     (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
 877     (description
 878      "This package provides tools to detect Gene Ontology and/or other user
 879 defined categories which are over/under represented in RNA-seq data.")
 880     (license license:lgpl2.0+)))
 881
 882 (define-public r-glimma
 883   (package
 884     (name "r-glimma")
 885     (version "1.10.1")
 886     (source
 887      (origin
 888        (method url-fetch)
 889        (uri (bioconductor-uri "Glimma" version))
 890        (sha256
 891         (base32
 892          "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
 893     (properties `((upstream-name . "Glimma")))
 894     (build-system r-build-system)
 895     (propagated-inputs
 896      `(("r-edger" ,r-edger)
 897        ("r-jsonlite" ,r-jsonlite)
 898        ("r-s4vectors" ,r-s4vectors)))
 899     (home-page "https://github.com/Shians/Glimma")
 900     (synopsis "Interactive HTML graphics")
 901     (description
 902      "This package generates interactive visualisations for analysis of
 903 RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
 904 HTML page.  The interactions are built on top of the popular static
 905 representations of analysis results in order to provide additional
 906 information.")
 907     (license license:lgpl3)))
 908
 909 (define-public r-rots
 910   (package
 911     (name "r-rots")
 912     (version "1.10.1")
 913     (source
 914      (origin
 915        (method url-fetch)
 916        (uri (bioconductor-uri "ROTS" version))
 917        (sha256
 918         (base32
 919          "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
 920     (properties `((upstream-name . "ROTS")))
 921     (build-system r-build-system)
 922     (propagated-inputs
 923      `(("r-biobase" ,r-biobase)
 924        ("r-rcpp" ,r-rcpp)))
 925     (home-page "https://bioconductor.org/packages/ROTS/")
 926     (synopsis "Reproducibility-Optimized Test Statistic")
 927     (description
 928      "This package provides tools for calculating the
 929 @dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
 930 in omics data.")
 931     (license license:gpl2+)))
 932
 933 (define-public r-plgem
 934   (package
 935     (name "r-plgem")
 936     (version "1.54.1")
 937     (source
 938      (origin
 939        (method url-fetch)
 940        (uri (bioconductor-uri "plgem" version))
 941        (sha256
 942         (base32
 943          "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
 944     (build-system r-build-system)
 945     (propagated-inputs
 946      `(("r-biobase" ,r-biobase)
 947        ("r-mass" ,r-mass)))
 948     (home-page "http://www.genopolis.it")
 949     (synopsis "Detect differential expression in microarray and proteomics datasets")
 950     (description
 951      "The Power Law Global Error Model (PLGEM) has been shown to faithfully
 952 model the variance-versus-mean dependence that exists in a variety of
 953 genome-wide datasets, including microarray and proteomics data.  The use of
 954 PLGEM has been shown to improve the detection of differentially expressed
 955 genes or proteins in these datasets.")
 956     (license license:gpl2)))
 957
 958 (define-public r-inspect
 959   (package
 960     (name "r-inspect")
 961     (version "1.12.1")
 962     (source
 963      (origin
 964        (method url-fetch)
 965        (uri (bioconductor-uri "INSPEcT" version))
 966        (sha256
 967         (base32
 968          "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
 969     (properties `((upstream-name . "INSPEcT")))
 970     (build-system r-build-system)
 971     (propagated-inputs
 972      `(("r-biobase" ,r-biobase)
 973        ("r-biocgenerics" ,r-biocgenerics)
 974        ("r-biocparallel" ,r-biocparallel)
 975        ("r-deseq2" ,r-deseq2)
 976        ("r-desolve" ,r-desolve)
 977        ("r-genomicalignments" ,r-genomicalignments)
 978        ("r-genomicfeatures" ,r-genomicfeatures)
 979        ("r-genomicranges" ,r-genomicranges)
 980        ("r-iranges" ,r-iranges)
 981        ("r-plgem" ,r-plgem)
 982        ("r-preprocesscore" ,r-preprocesscore)
 983        ("r-proc" ,r-proc)
 984        ("r-rootsolve" ,r-rootsolve)
 985        ("r-rsamtools" ,r-rsamtools)
 986        ("r-s4vectors" ,r-s4vectors)
 987        ("r-shiny" ,r-shiny)
 988        ("r-summarizedexperiment" ,r-summarizedexperiment)
 989        ("r-txdb-mmusculus-ucsc-mm9-knowngene"
 990         ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
 991     (home-page "https://bioconductor.org/packages/INSPEcT")
 992     (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
 993     (description
 994      "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
 995 Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
 996 order to evaluate synthesis, processing and degradation rates and assess via
 997 modeling the rates that determines changes in mature mRNA levels.")
 998     (license license:gpl2)))
 999
1000 (define-public r-dnabarcodes
1001   (package
1002     (name "r-dnabarcodes")
1003     (version "1.12.0")
1004     (source
1005      (origin
1006        (method url-fetch)
1007        (uri (bioconductor-uri "DNABarcodes" version))
1008        (sha256
1009         (base32
1010          "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
1011     (properties `((upstream-name . "DNABarcodes")))
1012     (build-system r-build-system)
1013     (propagated-inputs
1014      `(("r-bh" ,r-bh)
1015        ("r-matrix" ,r-matrix)
1016        ("r-rcpp" ,r-rcpp)))
1017     (home-page "https://bioconductor.org/packages/DNABarcodes")
1018     (synopsis "Create and analyze DNA barcodes")
1019     (description
1020      "This package offers tools to create DNA barcode sets capable of
1021 correcting insertion, deletion, and substitution errors.  Existing barcodes
1022 can be analyzed regarding their minimal, maximal and average distances between
1023 barcodes.  Finally, reads that start with a (possibly mutated) barcode can be
1024 demultiplexed, i.e. assigned to their original reference barcode.")
1025     (license license:gpl2)))
1026
1027 (define-public r-ruvseq
1028   (package
1029     (name "r-ruvseq")
1030     (version "1.16.1")
1031     (source
1032      (origin
1033        (method url-fetch)
1034        (uri (bioconductor-uri "RUVSeq" version))
1035        (sha256
1036         (base32
1037          "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
1038     (properties `((upstream-name . "RUVSeq")))
1039     (build-system r-build-system)
1040     (propagated-inputs
1041      `(("r-biobase" ,r-biobase)
1042        ("r-edaseq" ,r-edaseq)
1043        ("r-edger" ,r-edger)
1044        ("r-mass" ,r-mass)))
1045     (home-page "https://github.com/drisso/RUVSeq")
1046     (synopsis "Remove unwanted variation from RNA-Seq data")
1047     (description
1048      "This package implements methods to @dfn{remove unwanted variation} (RUV)
1049 of Risso et al. (2014) for the normalization of RNA-Seq read counts between
1050 samples.")
1051     (license license:artistic2.0)))
1052
1053 (define-public r-biocneighbors
1054   (package
1055     (name "r-biocneighbors")
1056     (version "1.0.0")
1057     (source
1058      (origin
1059        (method url-fetch)
1060        (uri (bioconductor-uri "BiocNeighbors" version))
1061        (sha256
1062         (base32
1063          "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
1064     (properties `((upstream-name . "BiocNeighbors")))
1065     (build-system r-build-system)
1066     (propagated-inputs
1067      `(("r-biocparallel" ,r-biocparallel)
1068        ("r-rcpp" ,r-rcpp)
1069        ("r-rcppannoy" ,r-rcppannoy)
1070        ("r-s4vectors" ,r-s4vectors)))
1071     (home-page "https://bioconductor.org/packages/BiocNeighbors")
1072     (synopsis "Nearest Neighbor Detection for Bioconductor packages")
1073     (description
1074      "This package implements exact and approximate methods for nearest
1075 neighbor detection, in a framework that allows them to be easily switched
1076 within Bioconductor packages or workflows.  The exact algorithm is implemented
1077 using pre-clustering with the k-means algorithm.  Functions are also provided
1078 to search for all neighbors within a given distance.  Parallelization is
1079 achieved for all methods using the BiocParallel framework.")
1080     (license license:gpl3)))
1081
1082 (define-public r-destiny
1083   (package
1084     (name "r-destiny")
1085     (version "2.12.0")
1086     (source
1087      (origin
1088        (method url-fetch)
1089        (uri (bioconductor-uri "destiny" version))
1090        (sha256
1091         (base32
1092          "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
1093     (build-system r-build-system)
1094     (propagated-inputs
1095      `(("r-biobase" ,r-biobase)
1096        ("r-biocgenerics" ,r-biocgenerics)
1097        ("r-fnn" ,r-fnn)
1098        ("r-ggthemes" ,r-ggthemes)
1099        ("r-hmisc" ,r-hmisc)
1100        ("r-igraph" ,r-igraph)
1101        ("r-matrix" ,r-matrix)
1102        ("r-proxy" ,r-proxy)
1103        ("r-rcpp" ,r-rcpp)
1104        ("r-rcppeigen" ,r-rcppeigen)
1105        ("r-scales" ,r-scales)
1106        ("r-scatterplot3d" ,r-scatterplot3d)
1107        ("r-smoother" ,r-smoother)
1108        ("r-summarizedexperiment" ,r-summarizedexperiment)
1109        ("r-vim" ,r-vim)))
1110     (home-page "https://bioconductor.org/packages/destiny/")
1111     (synopsis "Create and plot diffusion maps")
1112     (description "This package provides tools to create and plot diffusion
1113 maps.")
1114     ;; Any version of the GPL
1115     (license license:gpl3+)))
1116
1117 (define-public r-savr
1118   (package
1119     (name "r-savr")
1120     (version "1.20.0")
1121     (source
1122      (origin
1123        (method url-fetch)
1124        (uri (bioconductor-uri "savR" version))
1125        (sha256
1126         (base32
1127          "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
1128     (properties `((upstream-name . "savR")))
1129     (build-system r-build-system)
1130     (propagated-inputs
1131      `(("r-ggplot2" ,r-ggplot2)
1132        ("r-gridextra" ,r-gridextra)
1133        ("r-reshape2" ,r-reshape2)
1134        ("r-scales" ,r-scales)
1135        ("r-xml" ,r-xml)))
1136     (home-page "https://github.com/bcalder/savR")
1137     (synopsis "Parse and analyze Illumina SAV files")
1138     (description
1139      "This package provides tools to parse Illumina Sequence Analysis
1140 Viewer (SAV) files, access data, and generate QC plots.")
1141     (license license:agpl3+)))
1142
1143 (define-public r-chipexoqual
1144   (package
1145     (name "r-chipexoqual")
1146     (version "1.6.0")
1147     (source
1148      (origin
1149        (method url-fetch)
1150        (uri (bioconductor-uri "ChIPexoQual" version))
1151        (sha256
1152         (base32
1153          "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
1154     (properties `((upstream-name . "ChIPexoQual")))
1155     (build-system r-build-system)
1156     (propagated-inputs
1157      `(("r-biocparallel" ,r-biocparallel)
1158        ("r-biovizbase" ,r-biovizbase)
1159        ("r-broom" ,r-broom)
1160        ("r-data-table" ,r-data-table)
1161        ("r-dplyr" ,r-dplyr)
1162        ("r-genomeinfodb" ,r-genomeinfodb)
1163        ("r-genomicalignments" ,r-genomicalignments)
1164        ("r-genomicranges" ,r-genomicranges)
1165        ("r-ggplot2" ,r-ggplot2)
1166        ("r-hexbin" ,r-hexbin)
1167        ("r-iranges" ,r-iranges)
1168        ("r-rcolorbrewer" ,r-rcolorbrewer)
1169        ("r-rmarkdown" ,r-rmarkdown)
1170        ("r-rsamtools" ,r-rsamtools)
1171        ("r-s4vectors" ,r-s4vectors)
1172        ("r-scales" ,r-scales)
1173        ("r-viridis" ,r-viridis)))
1174     (home-page "https://github.com/keleslab/ChIPexoQual")
1175     (synopsis "Quality control pipeline for ChIP-exo/nexus data")
1176     (description
1177      "This package provides a quality control pipeline for ChIP-exo/nexus
1178 sequencing data.")
1179     (license license:gpl2+)))
1180
1181 (define-public r-dnacopy
1182   (package
1183     (name "r-dnacopy")
1184     (version "1.56.0")
1185     (source
1186      (origin
1187        (method url-fetch)
1188        (uri (bioconductor-uri "DNAcopy" version))
1189        (sha256
1190         (base32
1191          "04cqdqxhva66xwh1s2vffi56b9fcrqd4slcrvqasj5lp2rkjli82"))))
1192     (properties `((upstream-name . "DNAcopy")))
1193     (build-system r-build-system)
1194     (native-inputs `(("gfortran" ,gfortran)))
1195     (home-page "https://bioconductor.org/packages/DNAcopy")
1196     (synopsis "DNA copy number data analysis")
1197     (description
1198      "This package implements the @dfn{circular binary segmentation} (CBS)
1199 algorithm to segment DNA copy number data and identify genomic regions with
1200 abnormal copy number.")
1201     (license license:gpl2+)))
1202
1203 ;; This is a CRAN package, but it uncharacteristically depends on a
1204 ;; Bioconductor package.
1205 (define-public r-htscluster
1206   (package
1207     (name "r-htscluster")
1208     (version "2.0.8")
1209     (source
1210      (origin
1211        (method url-fetch)
1212        (uri (cran-uri "HTSCluster" version))
1213        (sha256
1214         (base32
1215          "0wnbfh6hdx8692jilgmv8sys1zm6fqc6mim7vvjhyqlmpm8gm0kg"))))
1216     (properties `((upstream-name . "HTSCluster")))
1217     (build-system r-build-system)
1218     (propagated-inputs
1219      `(("r-capushe" ,r-capushe)
1220        ("r-edger" ,r-edger)
1221        ("r-plotrix" ,r-plotrix)))
1222     (home-page "https://cran.r-project.org/web/packages/HTSCluster")
1223     (synopsis "Clustering high-throughput transcriptome sequencing (HTS) data")
1224     (description
1225      "This package provides a Poisson mixture model is implemented to cluster
1226 genes from high-throughput transcriptome sequencing (RNA-seq) data.  Parameter
1227 estimation is performed using either the EM or CEM algorithm, and the slope
1228 heuristics are used for model selection (i.e., to choose the number of
1229 clusters).")
1230     (license license:gpl3+)))