From cf9a29b24c990aeadb673d233b3ca686249b2b10 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Fri, 15 Jun 2018 08:21:17 +0200
Subject: gnu: Add r-genomicinteractions.

* gnu/packages/bioconductor.scm (r-genomicinteractions): New variable.
---
 gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 42 insertions(+), 2 deletions(-)

(limited to 'gnu/packages')

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 771f6a46d1..a6a8216ccb 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -24,10 +24,11 @@
   #: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 statistics)
-  #:use-module (gnu packages bioinformatics))
+  #:use-module (gnu packages graph)
+  #:use-module (gnu packages statistics))
 
 (define-public r-bsgenome-dmelanogaster-ucsc-dm6
   (package
@@ -635,3 +636,42 @@ parsing of genetic sequencing data from ribosome profiling experiments.")
 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 "1.14.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "GenomicInteractions" version))
+       (sha256
+        (base32
+         "0cnagprxj0b7p6s29iyhqwxj7hgmrh75gj52y4dlil790d1bmq2q"))))
+    (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)))
-- 
cgit v1.2.3