[jackhill/guix/guix.git] / gnu / packages / bioconductor.scm

;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018, 2019 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2017, 2018 Roel Janssen <roel@gnu.org>
;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.

(define-module (gnu packages bioconductor)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix download)
  #:use-module (guix build-system r)
  #:use-module (gnu packages)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages cran)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages web))

(define-public r-bsgenome-dmelanogaster-ucsc-dm6
  (package
    (name "r-bsgenome-dmelanogaster-ucsc-dm6")
    (version "1.4.1")
    (source (origin
              (method url-fetch)
              ;; We cannot use bioconductor-uri here because this tarball is
              ;; located under "data/annotation/" instead of "bioc/".
              (uri (string-append "https://www.bioconductor.org/packages/"
                                  "release/data/annotation/src/contrib/"
                                  "BSgenome.Dmelanogaster.UCSC.dm6_"
                                  version ".tar.gz"))
              (sha256
               (base32
                "1bhj0rdgf7lspw4xby9y9mf7v7jxxz8001bc8vw8kf04rjsx6060"))))
    (properties
     `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm6")))
    (build-system r-build-system)
    ;; As this package provides little more than a very large data file it
    ;; doesn't make sense to build substitutes.
    (arguments `(#:substitutable? #f))
    (propagated-inputs
     `(("r-bsgenome" ,r-bsgenome)))
    (home-page
     "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm6/")
    (synopsis "Full genome sequences for Fly")
    (description
     "This package provides full genome sequences for Drosophila
melanogaster (Fly) as provided by UCSC (dm6) and stored in Biostrings
objects.")
    (license license:artistic2.0)))

(define-public r-bsgenome-dmelanogaster-ucsc-dm3-masked
  (package
    (name "r-bsgenome-dmelanogaster-ucsc-dm3-masked")
    (version "1.3.99")
    (source (origin
              (method url-fetch)
              ;; We cannot use bioconductor-uri here because this tarball is
              ;; located under "data/annotation/" instead of "bioc/".
              (uri (string-append "http://www.bioconductor.org/packages/"
                                  "release/data/annotation/src/contrib/"
                                  "BSgenome.Dmelanogaster.UCSC.dm3.masked_"
                                  version ".tar.gz"))
              (sha256
               (base32
                "1756csb09f1br9rj1l3f08qyh4hlymdbd0cfn8x3fq39dn45m5ap"))))
    (properties
     `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3.masked")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-bsgenome" ,r-bsgenome)
       ("r-bsgenome-dmelanogaster-ucsc-dm3"
        ,r-bsgenome-dmelanogaster-ucsc-dm3)))
    (home-page "https://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3.masked/")
    (synopsis "Full masked genome sequences for Fly")
    (description
     "This package provides full masked genome sequences for Drosophila
melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in
Biostrings objects.  The sequences are the same as in
BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following
masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of
intra-contig ambiguities (AMB mask), (3) the mask of repeats from
RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats
Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by default.")
    (license license:artistic2.0)))

(define-public r-bsgenome-hsapiens-ucsc-hg19-masked
  (package
    (name "r-bsgenome-hsapiens-ucsc-hg19-masked")
    (version "1.3.99")
    (source (origin
              (method url-fetch)
              ;; We cannot use bioconductor-uri here because this tarball is
              ;; located under "data/annotation/" instead of "bioc/".
              (uri (string-append "http://www.bioconductor.org/packages/"
                                  "release/data/annotation/src/contrib/"
                                  "BSgenome.Hsapiens.UCSC.hg19.masked_"
                                  version ".tar.gz"))
              (sha256
               (base32
                "0452pyah0kv1vsrsjbrqw4k2rm8lc2vc771dzib45gnnfz86qxrr"))))
    (properties
     `((upstream-name . "BSgenome.Hsapiens.UCSC.hg19.masked")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-bsgenome" ,r-bsgenome)
       ("r-bsgenome-hsapiens-ucsc-hg19"
        ,r-bsgenome-hsapiens-ucsc-hg19)))
    (home-page "https://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/")
    (synopsis "Full masked genome sequences for Homo sapiens")
    (description
     "This package provides full genome sequences for Homo sapiens (Human) as
provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.  The
sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of
them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
Repeats Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by
default.")
    (license license:artistic2.0)))

(define-public r-bsgenome-mmusculus-ucsc-mm9-masked
  (package
    (name "r-bsgenome-mmusculus-ucsc-mm9-masked")
    (version "1.3.99")
    (source (origin
              (method url-fetch)
              ;; We cannot use bioconductor-uri here because this tarball is
              ;; located under "data/annotation/" instead of "bioc/".
              (uri (string-append "http://www.bioconductor.org/packages/"
                                  "release/data/annotation/src/contrib/"
                                  "BSgenome.Mmusculus.UCSC.mm9.masked_"
                                  version ".tar.gz"))
              (sha256
               (base32
                "00bpbm3havqcxr4g63zhllsbpd9q6svgihks7qp7x73nm4gvq7fn"))))
    (properties
     `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9.masked")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-bsgenome" ,r-bsgenome)
       ("r-bsgenome-mmusculus-ucsc-mm9"
        ,r-bsgenome-mmusculus-ucsc-mm9)))
    (home-page "http://bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9.masked/")
    (synopsis "Full masked genome sequences for Mouse")
    (description
     "This package provides full genome sequences for Mus musculus (Mouse) as
provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.  The
sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of
them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS
mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of
repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem
Repeats Finder (TRF mask).  Only the AGAPS and AMB masks are \"active\" by
default."  )
    (license license:artistic2.0)))

(define-public r-genelendatabase
  (package
    (name "r-genelendatabase")
    (version "1.16.0")
    (source
     (origin
       (method url-fetch)
       ;; We cannot use bioconductor-uri here because this tarball is
       ;; located under "data/experiment/" instead of "bioc/".
       (uri (string-append "https://bioconductor.org/packages/"
                           "release/data/experiment/src/contrib"
                           "/geneLenDataBase_" version ".tar.gz"))
       (sha256
        (base32
         "07mmmn53kb7v14msc13dsbm8ghssbvwcrhifrk15hn37bw2p4ja5"))))
    (properties
     `((upstream-name . "geneLenDataBase")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-rtracklayer" ,r-rtracklayer)
       ("r-genomicfeatures" ,r-genomicfeatures)))
    (home-page "https://bioconductor.org/packages/geneLenDataBase/")
    (synopsis "Lengths of mRNA transcripts for a number of genomes")
    (description
     "This package provides the lengths of mRNA transcripts for a number of
genomes and gene ID formats, largely based on the UCSC table browser.")
    (license license:lgpl2.0+)))

(define-public r-txdb-mmusculus-ucsc-mm9-knowngene
  (package
    (name "r-txdb-mmusculus-ucsc-mm9-knowngene")
    (version "3.2.2")
    (source (origin
              (method url-fetch)
              ;; We cannot use bioconductor-uri here because this tarball is
              ;; located under "data/annotation/" instead of "bioc/".
              (uri (string-append "https://bioconductor.org/packages/"
                                  "release/data/annotation/src/contrib"
                                  "/TxDb.Mmusculus.UCSC.mm9.knownGene_"
                                  version ".tar.gz"))
              (sha256
               (base32
                "16bjxy00363hf91ik2mqlqls86i07gia72qh92xc3l1ncch61mx2"))))
    (properties
     `((upstream-name . "TxDb.Mmusculus.UCSC.mm9.knownGene")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-genomicfeatures" ,r-genomicfeatures)
       ("r-annotationdbi" ,r-annotationdbi)))
    (home-page
     "https://bioconductor.org/packages/TxDb.Mmusculus.UCSC.mm9.knownGene/")
    (synopsis "Annotation package for mouse genome in TxDb format")
    (description
     "This package provides an annotation database of Mouse genome data.  It
is derived from the UCSC mm9 genome and based on the \"knownGene\" track.  The
database is exposed as a @code{TxDb} object.")
    (license license:artistic2.0)))

\f
(define-public r-annotate
  (package
    (name "r-annotate")
    (version "1.60.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "annotate" version))
       (sha256
        (base32
         "0p6c96lay23a67dyirgnwzm2yw22m592z780vy6p4nqwla8ha18n"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-annotationdbi" ,r-annotationdbi)
       ("r-biobase" ,r-biobase)
       ("r-biocgenerics" ,r-biocgenerics)
       ("r-dbi" ,r-dbi)
       ("r-rcurl" ,r-rcurl)
       ("r-xml" ,r-xml)
       ("r-xtable" ,r-xtable)))
    (home-page
     "https://bioconductor.org/packages/annotate")
    (synopsis "Annotation for microarrays")
    (description "This package provides R environments for the annotation of
microarrays.")
    (license license:artistic2.0)))

(define-public r-hpar
  (package
    (name "r-hpar")
    (version "1.24.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "hpar" version))
       (sha256
        (base32
         "1pm3k8apgynmdzv2d0chca3b636kcai3b1x861fyv1m3xs6msgxn"))))
    (build-system r-build-system)
    (home-page "https://bioconductor.org/packages/hpar/")
    (synopsis "Human Protein Atlas in R")
    (description "This package provides a simple interface to and data from
the Human Protein Atlas project.")
    (license license:artistic2.0)))

(define-public r-regioner
  (package
    (name "r-regioner")
    (version "1.14.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "regioneR" version))
       (sha256
        (base32
         "19la74swgzxp90z2nr3pzsgkxd7wp70zl6i2ipv3plg841f6k5zd"))))
    (properties `((upstream-name . "regioneR")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biostrings" ,r-biostrings)
       ("r-bsgenome" ,r-bsgenome)
       ("r-genomeinfodb" ,r-genomeinfodb)
       ("r-genomicranges" ,r-genomicranges)
       ("r-iranges" ,r-iranges)
       ("r-memoise" ,r-memoise)
       ("r-rtracklayer" ,r-rtracklayer)
       ("r-s4vectors" ,r-s4vectors)))
    (home-page "https://bioconductor.org/packages/regioneR/")
    (synopsis "Association analysis of genomic regions")
    (description "This package offers a statistical framework based on
customizable permutation tests to assess the association between genomic
region sets and other genomic features.")
    (license license:artistic2.0)))

(define-public r-diffbind
  (package
    (name "r-diffbind")
    (version "2.10.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "DiffBind" version))
       (sha256
        (base32
         "0j8pal40lr1gv8sss96hhkj7l1qn9sy4q4l2kqd4rfwl7qrcnfw5"))))
    (properties `((upstream-name . "DiffBind")))
    (build-system r-build-system)
    (inputs
     `(("zlib" ,zlib)))
    (propagated-inputs
     `(("r-amap" ,r-amap)
       ("r-biocparallel" ,r-biocparallel)
       ("r-deseq2" ,r-deseq2)
       ("r-dplyr" ,r-dplyr)
       ("r-edger" ,r-edger)
       ("r-genomicalignments" ,r-genomicalignments)
       ("r-genomicranges" ,r-genomicranges)
       ("r-ggplot2" ,r-ggplot2)
       ("r-ggrepel" ,r-ggrepel)
       ("r-gplots" ,r-gplots)
       ("r-iranges" ,r-iranges)
       ("r-lattice" ,r-lattice)
       ("r-limma" ,r-limma)
       ("r-locfit" ,r-locfit)
       ("r-rcolorbrewer" , r-rcolorbrewer)
       ("r-rcpp" ,r-rcpp)
       ("r-rsamtools" ,r-rsamtools)
       ("r-s4vectors" ,r-s4vectors)
       ("r-summarizedexperiment" ,r-summarizedexperiment)
       ("r-systempiper" ,r-systempiper)
       ("r-zlibbioc" ,r-zlibbioc)))
    (home-page "http://bioconductor.org/packages/DiffBind")
    (synopsis "Differential binding analysis of ChIP-Seq peak data")
    (description
     "This package computes differentially bound sites from multiple
ChIP-seq experiments using affinity (quantitative) data.  Also enables
occupancy (overlap) analysis and plotting functions.")
    (license license:artistic2.0)))

(define-public r-ripseeker
  (package
    (name "r-ripseeker")
    (version "1.22.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "RIPSeeker" version))
       (sha256
        (base32
         "1x2n1iyik4s67bxq0fl6fpf602k51g4pxjpjpxkgx1a5fsk61f2i"))))
    (properties `((upstream-name . "RIPSeeker")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-s4vectors" ,r-s4vectors)
       ("r-iranges" ,r-iranges)
       ("r-genomicranges" ,r-genomicranges)
       ("r-summarizedexperiment" ,r-summarizedexperiment)
       ("r-rsamtools" ,r-rsamtools)
       ("r-genomicalignments" ,r-genomicalignments)
       ("r-rtracklayer" ,r-rtracklayer)))
    (home-page "http://bioconductor.org/packages/RIPSeeker")
    (synopsis
     "Identifying protein-associated transcripts from RIP-seq experiments")
    (description
     "This package infers and discriminates RIP peaks from RIP-seq alignments
using two-state HMM with negative binomial emission probability.  While
RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides
a suite of bioinformatics tools integrated within this self-contained software
package comprehensively addressing issues ranging from post-alignments
processing to visualization and annotation.")
    (license license:gpl2)))

(define-public r-multtest
  (package
    (name "r-multtest")
    (version "2.38.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "multtest" version))
       (sha256
        (base32
         "0lq62jw81hz9k840969n5byj57pwd0jqga3hqvhb6abb3g10yz7k"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-survival" ,r-survival)
       ("r-biocgenerics" ,r-biocgenerics)
       ("r-biobase" ,r-biobase)
       ("r-mass" ,r-mass)))
    (home-page "http://bioconductor.org/packages/multtest")
    (synopsis "Resampling-based multiple hypothesis testing")
    (description
     "This package can do non-parametric bootstrap and permutation
resampling-based multiple testing procedures (including empirical Bayes
methods) for controlling the family-wise error rate (FWER), generalized
family-wise error rate (gFWER), tail probability of the proportion of
false positives (TPPFP), and false discovery rate (FDR).  Several choices
of bootstrap-based null distribution are implemented (centered, centered
and scaled, quantile-transformed).  Single-step and step-wise methods are
available.  Tests based on a variety of T- and F-statistics (including
T-statistics based on regression parameters from linear and survival models
as well as those based on correlation parameters) are included.  When probing
hypotheses with T-statistics, users may also select a potentially faster null
distribution which is multivariate normal with mean zero and variance
covariance matrix derived from the vector influence function.  Results are
reported in terms of adjusted P-values, confidence regions and test statistic
cutoffs.  The procedures are directly applicable to identifying differentially
expressed genes in DNA microarray experiments.")
    (license license:lgpl3)))

(define-public r-graph
  (package
    (name "r-graph")
    (version "1.60.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "graph" version))
              (sha256
               (base32
                "1kgnsm6f0vmb9qbkmmrnvxbwqc0gar17dq5gv1v10hrksw6mh64i"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocgenerics" ,r-biocgenerics)))
    (home-page "https://bioconductor.org/packages/graph")
    (synopsis "Handle graph data structures in R")
    (description
     "This package implements some simple graph handling capabilities for R.")
    (license license:artistic2.0)))

(define-public r-codedepends
  (package
    (name "r-codedepends")
    (version "0.6.5")
    (source
     (origin
       (method url-fetch)
       (uri (cran-uri "CodeDepends" version))
       (sha256
        (base32
         "0l7kiv3awx50glf5cs841b4zzsff1ml90f0zr868ygvwsr4ps1hq"))))
    (properties `((upstream-name . "CodeDepends")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-codetools" ,r-codetools)
       ("r-graph" ,r-graph)
       ("r-xml" ,r-xml)))
    (home-page "http://cran.r-project.org/web/packages/CodeDepends")
    (synopsis "Analysis of R code for reproducible research and code comprehension")
    (description
     "This package provides tools for analyzing R expressions or blocks of
code and determining the dependencies between them.  It focuses on R scripts,
but can be used on the bodies of functions.  There are many facilities
including the ability to summarize or get a high-level view of code,
determining dependencies between variables, code improvement suggestions.")
    ;; Any version of the GPL
    (license (list license:gpl2+ license:gpl3+))))

(define-public r-chippeakanno
  (package
    (name "r-chippeakanno")
    (version "3.16.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "ChIPpeakAnno" version))
       (sha256
        (base32
         "1x98d8iwrxjwdz1s5cnvi6flynw9gdkmara9gwf205qxgmy7j3a3"))))
    (properties `((upstream-name . "ChIPpeakAnno")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocgenerics" ,r-biocgenerics)
       ("r-biocmanager" ,r-biocmanager)
       ("r-biostrings" ,r-biostrings)
       ("r-delayedarray" ,r-delayedarray)
       ("r-go-db" ,r-go-db)
       ("r-biomart" ,r-biomart)
       ("r-bsgenome" ,r-bsgenome)
       ("r-genomicfeatures" ,r-genomicfeatures)
       ("r-genomicranges" ,r-genomicranges)
       ("r-genomeinfodb" ,r-genomeinfodb)
       ("r-iranges" ,r-iranges)
       ("r-matrixstats" ,r-matrixstats)
       ("r-annotationdbi" ,r-annotationdbi)
       ("r-limma" ,r-limma)
       ("r-multtest" ,r-multtest)
       ("r-rbgl" ,r-rbgl)
       ("r-graph" ,r-graph)
       ("r-regioner" ,r-regioner)
       ("r-dbi" ,r-dbi)
       ("r-ensembldb" ,r-ensembldb)
       ("r-biobase" ,r-biobase)
       ("r-s4vectors" ,r-s4vectors)
       ("r-seqinr" ,r-seqinr)
       ("r-idr" ,r-idr)
       ("r-genomicalignments" ,r-genomicalignments)
       ("r-summarizedexperiment" ,r-summarizedexperiment)
       ("r-rsamtools" ,r-rsamtools)
       ("r-venndiagram" ,r-venndiagram)))
    (home-page "http://bioconductor.org/packages/ChIPpeakAnno")
    (synopsis "Peaks annotation from ChIP-seq and ChIP-chip experiments")
    (description
     "The package includes functions to retrieve the sequences around the peak,
obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or
custom features such as most conserved elements and other transcription factor
binding sites supplied by users.  Starting 2.0.5, new functions have been added
for finding the peaks with bi-directional promoters with summary statistics
(peaksNearBDP), for summarizing the occurrence of motifs in peaks
(summarizePatternInPeaks) and for adding other IDs to annotated peaks or
enrichedGO (addGeneIDs).")
    (license license:gpl2+)))

(define-public r-marray
  (package
    (name "r-marray")
    (version "1.60.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "marray" version))
              (sha256
               (base32 "1sh7l3c28x6zhdv99c9x05ii2yxmh9alkazp98kdi4fdb23rlzky"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-limma" ,r-limma)))
    (home-page "http://bioconductor.org/packages/marray")
    (synopsis "Exploratory analysis for two-color spotted microarray data")
    (description "This package contains class definitions for two-color spotted
microarray data.  It also includes fuctions for data input, diagnostic plots,
normalization and quality checking.")
    (license license:lgpl2.0+)))

(define-public r-cghbase
  (package
   (name "r-cghbase")
   (version "1.42.0")
   (source (origin
            (method url-fetch)
            (uri (bioconductor-uri "CGHbase" version))
            (sha256
             (base32 "0ghxp49xdi09p3f2qwrdrq2p4qjafj4z1rr08ycgbf11gb22h1sc"))))
   (properties `((upstream-name . "CGHbase")))
   (build-system r-build-system)
   (propagated-inputs
    `(("r-biobase" ,r-biobase)
      ("r-marray" ,r-marray)))
   (home-page "http://bioconductor.org/packages/CGHbase")
   (synopsis "Base functions and classes for arrayCGH data analysis")
   (description "This package contains functions and classes that are needed by
the @code{arrayCGH} packages.")
   (license license:gpl2+)))

(define-public r-cghcall
  (package
   (name "r-cghcall")
   (version "2.44.0")
   (source (origin
            (method url-fetch)
            (uri (bioconductor-uri "CGHcall" version))
            (sha256
             (base32 "1k65kaiqvjyllzbpa2367n6f6kkmsy463kpflzs66hqhx2fshsmi"))))
   (properties `((upstream-name . "CGHcall")))
   (build-system r-build-system)
   (propagated-inputs
    `(("r-biobase" ,r-biobase)
      ("r-cghbase" ,r-cghbase)
      ("r-impute" ,r-impute)
      ("r-dnacopy" ,r-dnacopy)
      ("r-snowfall" ,r-snowfall)))
   (home-page "http://bioconductor.org/packages/CGHcall")
   (synopsis "Base functions and classes for arrayCGH data analysis")
   (description "This package contains functions and classes that are needed by
@code{arrayCGH} packages.")
   (license license:gpl2+)))

(define-public r-qdnaseq
  (package
    (name "r-qdnaseq")
    (version "1.18.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "QDNAseq" version))
              (sha256
               (base32 "04ff9nbckzrlb45mr2j0c3mlh1wcggq5bbl81zklhq203c5x1wc2"))))
    (properties `((upstream-name . "QDNAseq")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-biocparallel" ,r-biocparallel)
       ("r-cghbase" ,r-cghbase)
       ("r-cghcall" ,r-cghcall)
       ("r-dnacopy" ,r-dnacopy)
       ("r-genomicranges" ,r-genomicranges)
       ("r-iranges" ,r-iranges)
       ("r-matrixstats" ,r-matrixstats)
       ("r-r-utils" ,r-r-utils)
       ("r-rsamtools" ,r-rsamtools)))
    (home-page "http://bioconductor.org/packages/QDNAseq")
    (synopsis "Quantitative DNA sequencing for chromosomal aberrations")
    (description "The genome is divided into non-overlapping fixed-sized bins,
number of sequence reads in each counted, adjusted with a simultaneous
two-dimensional loess correction for sequence mappability and GC content, and
filtered to remove spurious regions in the genome.  Downstream steps of
segmentation and calling are also implemented via packages DNAcopy and CGHcall,
respectively.")
    (license license:gpl2+)))

(define-public r-bayseq
  (package
    (name "r-bayseq")
    (version "2.16.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "baySeq" version))
       (sha256
        (base32
         "0f6yckihm5cwh3dycv2g54hf7nddhcqya4yrqwbir96y5k1d1km5"))))
    (properties `((upstream-name . "baySeq")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-abind" ,r-abind)
       ("r-edger" ,r-edger)
       ("r-genomicranges" ,r-genomicranges)))
    (home-page "https://bioconductor.org/packages/baySeq/")
    (synopsis "Bayesian analysis of differential expression patterns in count data")
    (description
     "This package identifies differential expression in high-throughput count
data, such as that derived from next-generation sequencing machines,
calculating estimated posterior likelihoods of differential expression (or
more complex hypotheses) via empirical Bayesian methods.")
    (license license:gpl3)))

(define-public r-chipcomp
  (package
    (name "r-chipcomp")
    (version "1.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "ChIPComp" version))
       (sha256
        (base32
         "1sypdsvwzssraanlhddhzpf9p0xs3qlflc0hp7yfbp0aplsifx85"))))
    (properties `((upstream-name . "ChIPComp")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocgenerics" ,r-biocgenerics)
       ("r-bsgenome-hsapiens-ucsc-hg19" ,r-bsgenome-hsapiens-ucsc-hg19)
       ("r-bsgenome-mmusculus-ucsc-mm9" ,r-bsgenome-mmusculus-ucsc-mm9)
       ("r-genomeinfodb" ,r-genomeinfodb)
       ("r-genomicranges" ,r-genomicranges)
       ("r-iranges" ,r-iranges)
       ("r-limma" ,r-limma)
       ("r-rsamtools" ,r-rsamtools)
       ("r-rtracklayer" ,r-rtracklayer)
       ("r-s4vectors" ,r-s4vectors)))
    (home-page "https://bioconductor.org/packages/ChIPComp")
    (synopsis "Quantitative comparison of multiple ChIP-seq datasets")
    (description
     "ChIPComp implements a statistical method for quantitative comparison of
multiple ChIP-seq datasets.  It detects differentially bound sharp binding
sites across multiple conditions considering matching control in ChIP-seq
datasets.")
    ;; Any version of the GPL.
    (license license:gpl3+)))

(define-public r-riboprofiling
  (package
    (name "r-riboprofiling")
    (version "1.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "RiboProfiling" version))
       (sha256
        (base32
         "1njvkd1khmf3rbp3dkz5z63wp79z4wmk4kzd3p3amky3w5by070z"))))
    (properties `((upstream-name . "RiboProfiling")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocgenerics" ,r-biocgenerics)
       ("r-biostrings" ,r-biostrings)
       ("r-data-table" ,r-data-table)
       ("r-genomeinfodb" ,r-genomeinfodb)
       ("r-genomicalignments" ,r-genomicalignments)
       ("r-genomicfeatures" ,r-genomicfeatures)
       ("r-genomicranges" ,r-genomicranges)
       ("r-ggbio" ,r-ggbio)
       ("r-ggplot2" ,r-ggplot2)
       ("r-iranges" ,r-iranges)
       ("r-plyr" ,r-plyr)
       ("r-reshape2" ,r-reshape2)
       ("r-rsamtools" ,r-rsamtools)
       ("r-rtracklayer" ,r-rtracklayer)
       ("r-s4vectors" ,r-s4vectors)
       ("r-sqldf" ,r-sqldf)))
    (home-page "https://bioconductor.org/packages/RiboProfiling/")
    (synopsis "Ribosome profiling data analysis")
    (description "Starting with a BAM file, this package provides the
necessary functions for quality assessment, read start position recalibration,
the counting of genomic sequence reads on CDS, 3'UTR, and 5'UTR, and plotting
of count data: pairs, log fold-change, codon frequency and coverage
assessment, principal component analysis on codon coverage.")
    (license license:gpl3)))

(define-public r-riboseqr
  (package
    (name "r-riboseqr")
    (version "1.16.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "riboSeqR" version))
       (sha256
        (base32
         "1nacsbsz77fw4a10nqj2ncsf25q3aaa0gd5w1q0ray2prx7qmlqb"))))
    (properties `((upstream-name . "riboSeqR")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-abind" ,r-abind)
       ("r-bayseq" ,r-bayseq)
       ("r-genomeinfodb" ,r-genomeinfodb)
       ("r-genomicranges" ,r-genomicranges)
       ("r-iranges" ,r-iranges)
       ("r-rsamtools" ,r-rsamtools)
       ("r-seqlogo" ,r-seqlogo)))
    (home-page "https://bioconductor.org/packages/riboSeqR/")
    (synopsis "Analysis of sequencing data from ribosome profiling experiments")
    (description
     "This package provides plotting functions, frameshift detection and
parsing of genetic sequencing data from ribosome profiling experiments.")
    (license license:gpl3)))

(define-public r-interactionset
  (package
    (name "r-interactionset")
    (version "1.10.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "InteractionSet" version))
       (sha256
        (base32
         "0wirfhmpmkmnmhbqslw4bzvi2msqyqpjy1rrwr5qbd9k5rhx3bzb"))))
    (properties
     `((upstream-name . "InteractionSet")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocgenerics" ,r-biocgenerics)
       ("r-genomeinfodb" ,r-genomeinfodb)
       ("r-genomicranges" ,r-genomicranges)
       ("r-iranges" ,r-iranges)
       ("r-matrix" ,r-matrix)
       ("r-rcpp" ,r-rcpp)
       ("r-s4vectors" ,r-s4vectors)
       ("r-summarizedexperiment" ,r-summarizedexperiment)))
    (home-page "https://bioconductor.org/packages/InteractionSet")
    (synopsis "Base classes for storing genomic interaction data")
    (description
     "This packages provides the @code{GInteractions},
@code{InteractionSet} and @code{ContactMatrix} objects and associated methods
for storing and manipulating genomic interaction data from Hi-C and ChIA-PET
experiments.")
    (license license:gpl3)))

(define-public r-genomicinteractions
  (package
    (name "r-genomicinteractions")
    (version "1.16.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "GenomicInteractions" version))
       (sha256
        (base32
         "0zy5isp2lqpjm0n0n1gly5bs4izn22yciibyqrnlrr60rmn5s67q"))))
    (properties
     `((upstream-name . "GenomicInteractions")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-biocgenerics" ,r-biocgenerics)
       ("r-data-table" ,r-data-table)
       ("r-dplyr" ,r-dplyr)
       ("r-genomeinfodb" ,r-genomeinfodb)
       ("r-genomicranges" ,r-genomicranges)
       ("r-ggplot2" ,r-ggplot2)
       ("r-gridextra" ,r-gridextra)
       ("r-gviz" ,r-gviz)
       ("r-igraph" ,r-igraph)
       ("r-interactionset" ,r-interactionset)
       ("r-iranges" ,r-iranges)
       ("r-rsamtools" ,r-rsamtools)
       ("r-rtracklayer" ,r-rtracklayer)
       ("r-s4vectors" ,r-s4vectors)
       ("r-stringr" ,r-stringr)))
    (home-page "https://github.com/ComputationalRegulatoryGenomicsICL/GenomicInteractions/")
    (synopsis "R package for handling genomic interaction data")
    (description
     "This R package provides tools for handling genomic interaction data,
such as ChIA-PET/Hi-C, annotating genomic features with interaction
information and producing various plots and statistics.")
    (license license:gpl3)))

(define-public r-ctc
  (package
    (name "r-ctc")
    (version "1.56.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "ctc" version))
       (sha256
        (base32
         "0yp7c0abk48jx1wf8n1gawh7dm15idahqc8va24v8cm0bzxgnmh2"))))
    (build-system r-build-system)
    (propagated-inputs `(("r-amap" ,r-amap)))
    (home-page "https://bioconductor.org/packages/ctc/")
    (synopsis "Cluster and tree conversion")
    (description
     "This package provides tools for exporting and importing classification
trees and clusters to other programs.")
    (license license:gpl2)))

(define-public r-goseq
  (package
    (name "r-goseq")
    (version "1.34.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "goseq" version))
       (sha256
        (base32
         "1j87j98cajcjqabv6rb6zmcqxsqxxhbb3w60w1iink4rhsh8m3mn"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-annotationdbi" ,r-annotationdbi)
       ("r-biasedurn" ,r-biasedurn)
       ("r-biocgenerics" ,r-biocgenerics)
       ("r-genelendatabase" ,r-genelendatabase)
       ("r-go-db" ,r-go-db)
       ("r-mgcv" ,r-mgcv)))
    (home-page "https://bioconductor.org/packages/goseq/")
    (synopsis "Gene Ontology analyser for RNA-seq and other length biased data")
    (description
     "This package provides tools to detect Gene Ontology and/or other user
defined categories which are over/under represented in RNA-seq data.")
    (license license:lgpl2.0+)))

(define-public r-glimma
  (package
    (name "r-glimma")
    (version "1.10.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "Glimma" version))
       (sha256
        (base32
         "1ihrww55sa7ipi1rpp0rmn081sbqdwdmm5mz30zfrjr1xxqcdbcv"))))
    (properties `((upstream-name . "Glimma")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-edger" ,r-edger)
       ("r-jsonlite" ,r-jsonlite)
       ("r-s4vectors" ,r-s4vectors)))
    (home-page "https://github.com/Shians/Glimma")
    (synopsis "Interactive HTML graphics")
    (description
     "This package generates interactive visualisations for analysis of
RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an
HTML page.  The interactions are built on top of the popular static
representations of analysis results in order to provide additional
information.")
    (license license:lgpl3)))

(define-public r-rots
  (package
    (name "r-rots")
    (version "1.10.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "ROTS" version))
       (sha256
        (base32
         "1d5ggkk47xybcaizfy756qimbf2falg9cld46mhqjp3xfbfvzsg6"))))
    (properties `((upstream-name . "ROTS")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-rcpp" ,r-rcpp)))
    (home-page "https://bioconductor.org/packages/ROTS/")
    (synopsis "Reproducibility-Optimized Test Statistic")
    (description
     "This package provides tools for calculating the
@dfn{Reproducibility-Optimized Test Statistic} (ROTS) for differential testing
in omics data.")
    (license license:gpl2+)))

(define-public r-plgem
  (package
    (name "r-plgem")
    (version "1.54.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "plgem" version))
       (sha256
        (base32
         "1330635db3p8xm5y8fwrk1l37r6bgypsq70s3rx954i775zp6szg"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-mass" ,r-mass)))
    (home-page "http://www.genopolis.it")
    (synopsis "Detect differential expression in microarray and proteomics datasets")
    (description
     "The Power Law Global Error Model (PLGEM) has been shown to faithfully
model the variance-versus-mean dependence that exists in a variety of
genome-wide datasets, including microarray and proteomics data.  The use of
PLGEM has been shown to improve the detection of differentially expressed
genes or proteins in these datasets.")
    (license license:gpl2)))

(define-public r-inspect
  (package
    (name "r-inspect")
    (version "1.12.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "INSPEcT" version))
       (sha256
        (base32
         "07q5msw9rnamx957mbiawnv3p9kr5ahwawzvv9xzla7d3lkk62xp"))))
    (properties `((upstream-name . "INSPEcT")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-biocgenerics" ,r-biocgenerics)
       ("r-biocparallel" ,r-biocparallel)
       ("r-deseq2" ,r-deseq2)
       ("r-desolve" ,r-desolve)
       ("r-genomicalignments" ,r-genomicalignments)
       ("r-genomicfeatures" ,r-genomicfeatures)
       ("r-genomicranges" ,r-genomicranges)
       ("r-iranges" ,r-iranges)
       ("r-plgem" ,r-plgem)
       ("r-preprocesscore" ,r-preprocesscore)
       ("r-proc" ,r-proc)
       ("r-rootsolve" ,r-rootsolve)
       ("r-rsamtools" ,r-rsamtools)
       ("r-s4vectors" ,r-s4vectors)
       ("r-shiny" ,r-shiny)
       ("r-summarizedexperiment" ,r-summarizedexperiment)
       ("r-txdb-mmusculus-ucsc-mm9-knowngene"
        ,r-txdb-mmusculus-ucsc-mm9-knowngene)))
    (home-page "https://bioconductor.org/packages/INSPEcT")
    (synopsis "Analysis of 4sU-seq and RNA-seq time-course data")
    (description
     "INSPEcT (INference of Synthesis, Processing and dEgradation rates in
Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in
order to evaluate synthesis, processing and degradation rates and assess via
modeling the rates that determines changes in mature mRNA levels.")
    (license license:gpl2)))

(define-public r-dnabarcodes
  (package
    (name "r-dnabarcodes")
    (version "1.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "DNABarcodes" version))
       (sha256
        (base32
         "0g6j7ish0fk9jcib94wssjgp1m8ldcp42hyyg1ypr945fa3xghx0"))))
    (properties `((upstream-name . "DNABarcodes")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-bh" ,r-bh)
       ("r-matrix" ,r-matrix)
       ("r-rcpp" ,r-rcpp)))
    (home-page "https://bioconductor.org/packages/DNABarcodes")
    (synopsis "Create and analyze DNA barcodes")
    (description
     "This package offers tools to create DNA barcode sets capable of
correcting insertion, deletion, and substitution errors.  Existing barcodes
can be analyzed regarding their minimal, maximal and average distances between
barcodes.  Finally, reads that start with a (possibly mutated) barcode can be
demultiplexed, i.e. assigned to their original reference barcode.")
    (license license:gpl2)))

(define-public r-ruvseq
  (package
    (name "r-ruvseq")
    (version "1.16.1")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "RUVSeq" version))
       (sha256
        (base32
         "0qk7q3ab7k133divfkp54zsmvsmb9p8r09pkh2caswrzrn8achzv"))))
    (properties `((upstream-name . "RUVSeq")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-edaseq" ,r-edaseq)
       ("r-edger" ,r-edger)
       ("r-mass" ,r-mass)))
    (home-page "https://github.com/drisso/RUVSeq")
    (synopsis "Remove unwanted variation from RNA-Seq data")
    (description
     "This package implements methods to @dfn{remove unwanted variation} (RUV)
of Risso et al. (2014) for the normalization of RNA-Seq read counts between
samples.")
    (license license:artistic2.0)))

(define-public r-biocneighbors
  (package
    (name "r-biocneighbors")
    (version "1.0.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "BiocNeighbors" version))
       (sha256
        (base32
         "1fsb96acidlxwf0h65xv7fnwdi58ckmq00gmwykrlawh88wgn1ll"))))
    (properties `((upstream-name . "BiocNeighbors")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocparallel" ,r-biocparallel)
       ("r-rcpp" ,r-rcpp)
       ("r-rcppannoy" ,r-rcppannoy)
       ("r-s4vectors" ,r-s4vectors)))
    (home-page "https://bioconductor.org/packages/BiocNeighbors")
    (synopsis "Nearest Neighbor Detection for Bioconductor packages")
    (description
     "This package implements exact and approximate methods for nearest
neighbor detection, in a framework that allows them to be easily switched
within Bioconductor packages or workflows.  The exact algorithm is implemented
using pre-clustering with the k-means algorithm.  Functions are also provided
to search for all neighbors within a given distance.  Parallelization is
achieved for all methods using the BiocParallel framework.")
    (license license:gpl3)))

(define-public r-destiny
  (package
    (name "r-destiny")
    (version "2.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "destiny" version))
       (sha256
        (base32
         "1iay17mrhsfmpwl920rh1nip5b6ybva4h6bna0yld04paq5yva67"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("r-biocgenerics" ,r-biocgenerics)
       ("r-fnn" ,r-fnn)
       ("r-ggthemes" ,r-ggthemes)
       ("r-hmisc" ,r-hmisc)
       ("r-igraph" ,r-igraph)
       ("r-matrix" ,r-matrix)
       ("r-proxy" ,r-proxy)
       ("r-rcpp" ,r-rcpp)
       ("r-rcppeigen" ,r-rcppeigen)
       ("r-scales" ,r-scales)
       ("r-scatterplot3d" ,r-scatterplot3d)
       ("r-smoother" ,r-smoother)
       ("r-summarizedexperiment" ,r-summarizedexperiment)
       ("r-vim" ,r-vim)))
    (home-page "https://bioconductor.org/packages/destiny/")
    (synopsis "Create and plot diffusion maps")
    (description "This package provides tools to create and plot diffusion
maps.")
    ;; Any version of the GPL
    (license license:gpl3+)))

(define-public r-savr
  (package
    (name "r-savr")
    (version "1.20.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "savR" version))
       (sha256
        (base32
         "13bwq2a2pygdkmhrcmvz525wsi5i01j911711zgs6x93wj20b2w7"))))
    (properties `((upstream-name . "savR")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-ggplot2" ,r-ggplot2)
       ("r-gridextra" ,r-gridextra)
       ("r-reshape2" ,r-reshape2)
       ("r-scales" ,r-scales)
       ("r-xml" ,r-xml)))
    (home-page "https://github.com/bcalder/savR")
    (synopsis "Parse and analyze Illumina SAV files")
    (description
     "This package provides tools to parse Illumina Sequence Analysis
Viewer (SAV) files, access data, and generate QC plots.")
    (license license:agpl3+)))

(define-public r-chipexoqual
  (package
    (name "r-chipexoqual")
    (version "1.6.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "ChIPexoQual" version))
       (sha256
        (base32
         "1773bpiybn4g9jlv46z29x19q4dpcvn7lairr3lq5pdqbqmz5hnp"))))
    (properties `((upstream-name . "ChIPexoQual")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocparallel" ,r-biocparallel)
       ("r-biovizbase" ,r-biovizbase)
       ("r-broom" ,r-broom)
       ("r-data-table" ,r-data-table)
       ("r-dplyr" ,r-dplyr)
       ("r-genomeinfodb" ,r-genomeinfodb)
       ("r-genomicalignments" ,r-genomicalignments)
       ("r-genomicranges" ,r-genomicranges)
       ("r-ggplot2" ,r-ggplot2)
       ("r-hexbin" ,r-hexbin)
       ("r-iranges" ,r-iranges)
       ("r-rcolorbrewer" ,r-rcolorbrewer)
       ("r-rmarkdown" ,r-rmarkdown)
       ("r-rsamtools" ,r-rsamtools)
       ("r-s4vectors" ,r-s4vectors)
       ("r-scales" ,r-scales)
       ("r-viridis" ,r-viridis)))
    (home-page "https://github.com/keleslab/ChIPexoQual")
    (synopsis "Quality control pipeline for ChIP-exo/nexus data")
    (description
     "This package provides a quality control pipeline for ChIP-exo/nexus
sequencing data.")
    (license license:gpl2+)))