;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
;;;
;;; 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-hpar
  (package
    (name "r-hpar")
    (version "1.20.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "hpar" version))
       (sha256
        (base32
         "0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8"))))
    (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 "1.10.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "regioneR" version))
       (sha256
        (base32
         "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp"))))
    (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)))
    (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 "2.6.6")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "DiffBind" version))
       (sha256
        (base32
         "1sm5h6nq77hjfis6kr1nqyizcxgfz87dgpqc4fxlfqkmsd9n3vkp"))))
    (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-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-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 "1.18.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "RIPSeeker" version))
       (sha256
        (base32
         "0bqkzwrncww7il36273chkd3gfxmii7p566ycki9qij419pwr35y"))))
    (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 "2.34.0")
    (source
     (origin
       (method url-fetch)
       (uri (bioconductor-uri "multtest" version))
       (sha256
        (base32
         "0n11rd49xl2vn3ldmfips7d3yb70l8npjcqsxyswr9ypjhgzkv9j"))))
    (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)))