;;; 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 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)))