;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 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 cran)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages bioinformatics))

(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-hpar
  (package
    (name "r-hpar")
    (version "1.22.2")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "hpar" version))
       (sha256
        (base32
         "1b72hvzasf6q739gmx6jblbzzyq22l7crrkbbfkihv3v7s94g388"))))
    (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 "1.12.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "regioneR" version))
       (sha256
        (base32
         "09bzlaqdgy7wmzly3zc9y2da50d07mlixlnpaxdxpiwdk8qmhxsb"))))
    (properties `((upstream-name . "regioneR")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-memoise" ,r-memoise)
       ("r-genomicranges" ,r-genomicranges)
       ("r-bsgenome" ,r-bsgenome)
       ("r-rtracklayer" ,r-rtracklayer)
       ("r-genomeinfodb" ,r-genomeinfodb)
       ("r-iranges" ,r-iranges)
       ("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 "2.8.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "DiffBind" version))
       (sha256
        (base32
         "1w1hybzd732ccg3q8zhirwfilq8sx3frv1x98zfyj3svzw98fish"))))
    (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 "1.20.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "RIPSeeker" version))
       (sha256
        (base32
         "0y9cvzqslfxj3z9mnp47mknff0pky2g5x8x1z1s5yjcx35q89xfi"))))
    (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 "2.36.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "multtest" version))
       (sha256
        (base32
         "11949h2kglw13x8haaj4clg4jim1mwh5n98n9zxp9mmgn01z1lp0"))))
    (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-chippeakanno
  (package
    (name "r-chippeakanno")
    (version "3.14.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "ChIPpeakAnno" version))
       (sha256
        (base32
         "1kcnc3cnmrhdk1x7q3y6zsz09pgd3xn9xy1hfbxz48cajlb18ad0"))))
    (properties `((upstream-name . "ChIPpeakAnno")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biocgenerics" ,r-biocgenerics)
       ("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-biocinstaller" ,r-biocinstaller)
       ("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 "1.56.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "marray" version))
              (sha256
               (base32 "14c93i86yc7jn4ax8p4l0z6v9xisw1bv7gzb4a0gbxhxn7mddaic"))))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("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 "1.38.0")
   (source (origin
            (method url-fetch)
            (uri (bioconductor-uri "CGHbase" version))
            (sha256
             (base32 "0fynvcsjdbgp69i0nxrc8ni58rhb1kx9k5r3nb91n9i8s43gjqlm"))))
   (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 "2.40.0")
   (source (origin
            (method url-fetch)
            (uri (bioconductor-uri "CGHcall" version))
            (sha256
             (base32 "11pi6awz3858yb4s0z3qf3kcmsdgp6d4aj41g4lfix1sv5amllch"))))
   (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 "1.14.0")
    (source (origin
              (method url-fetch)
              (uri (bioconductor-uri "QDNAseq" version))
              (sha256
               (base32 "0lgbv4s0xqgrs7q6ynb3c273sf7pyrp51jnc8ravq1z5g0a2zshy"))))
    (properties `((upstream-name . "QDNAseq")))
    (build-system r-build-system)
    (propagated-inputs
     `(("r-biobase" ,r-biobase)
       ("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+)))