gnu/packages/bioconductor.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2018 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2018 Roel Janssen <roel@gnu.org>
   4 ;;;
   5 ;;; This file is part of GNU Guix.
   6 ;;;
   7 ;;; GNU Guix is free software; you can redistribute it and/or modify it
   8 ;;; under the terms of the GNU General Public License as published by
   9 ;;; the Free Software Foundation; either version 3 of the License, or (at
  10 ;;; your option) any later version.
  11 ;;;
  12 ;;; GNU Guix is distributed in the hope that it will be useful, but
  13 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  14 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  15 ;;; GNU General Public License for more details.
  16 ;;;
  17 ;;; You should have received a copy of the GNU General Public License
  18 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  19
  20 (define-module (gnu packages bioconductor)
  21   #:use-module ((guix licenses) #:prefix license:)
  22   #:use-module (guix packages)
  23   #:use-module (guix download)
  24   #:use-module (guix build-system r)
  25   #:use-module (gnu packages)
  26   #:use-module (gnu packages statistics)
  27   #:use-module (gnu packages bioinformatics))
  28
  29 (define-public r-hpar
  30   (package
  31     (name "r-hpar")
  32     (version "1.20.0")
  33     (source
  34      (origin
  35        (method url-fetch)
  36        (uri (bioconductor-uri "hpar" version))
  37        (sha256
  38         (base32
  39          "0s5v79mgxdx862v1jrdf5pdap81nz5vjx25ni8s3sl97ldckf6j8"))))
  40     (build-system r-build-system)
  41     (home-page "https://bioconductor.org/packages/hpar/")
  42     (synopsis "Human Protein Atlas in R")
  43     (description "This package provides a simple interface to and data from
  44 the Human Protein Atlas project.")
  45     (license license:artistic2.0)))
  46
  47 (define-public r-regioner
  48   (package
  49     (name "r-regioner")
  50     (version "1.10.0")
  51     (source
  52      (origin
  53        (method url-fetch)
  54        (uri (bioconductor-uri "regioneR" version))
  55        (sha256
  56         (base32
  57          "1vprp3l929hwzmvgskbhawfgnrymwc9n2rxd16rgagnv1dxnjxfp"))))
  58     (properties `((upstream-name . "regioneR")))
  59     (build-system r-build-system)
  60     (propagated-inputs
  61      `(("r-memoise" ,r-memoise)
  62        ("r-genomicranges" ,r-genomicranges)
  63        ("r-bsgenome" ,r-bsgenome)
  64        ("r-rtracklayer" ,r-rtracklayer)
  65        ("r-genomeinfodb" ,r-genomeinfodb)
  66        ("r-iranges" ,r-iranges)))
  67     (home-page "https://bioconductor.org/packages/regioneR/")
  68     (synopsis "Association analysis of genomic regions")
  69     (description "This package offers a statistical framework based on
  70 customizable permutation tests to assess the association between genomic
  71 region sets and other genomic features.")
  72     (license license:artistic2.0)))