From 755733a3fee60097735ac85a388b582b30e68b88 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Tue, 23 Jun 2020 13:41:36 +0200
Subject: [PATCH] gnu: Add r-fourcseq.
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* gnu/packages/cran.scm (r-fourcseq): New variable.

Co-authored-by: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
---
 gnu/packages/cran.scm | 44 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

diff --git a/gnu/packages/cran.scm b/gnu/packages/cran.scm
index ac246bd123..e81d11e6e5 100644
--- a/gnu/packages/cran.scm
+++ b/gnu/packages/cran.scm
@@ -22230,3 +22230,47 @@ (define-public r-lsd
 Try a demo of the LSD by running @code{demotour()}.")
     ;; Either version
     (license (list license:gpl2 license:gpl3))))
+
+(define-public r-fourcseq
+  (package
+    (name "r-fourcseq")
+    (version "1.21.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "FourCSeq" version))
+       (sha256
+        (base32 "0lhcjw2hmmdafq52c5fvpm1crnzynbslamzh7r6ygifmzaz2pa8x"))))
+    (properties `((upstream-name . "FourCSeq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     `(("r-biobase" ,r-biobase)
+       ("r-biostrings" ,r-biostrings)
+       ("r-deseq2" ,r-deseq2)
+       ("r-fda" ,r-fda)
+       ("r-genomicalignments" ,r-genomicalignments)
+       ("r-genomicranges" ,r-genomicranges)
+       ("r-ggbio" ,r-ggbio)
+       ("r-ggplot2" ,r-ggplot2)
+       ("r-gtools" ,r-gtools)
+       ("r-lsd" ,r-lsd)
+       ("r-matrix" ,r-matrix)
+       ("r-reshape2" ,r-reshape2)
+       ("r-rsamtools" ,r-rsamtools)
+       ("r-rtracklayer" ,r-rtracklayer)
+       ("r-summarizedexperiment" ,r-summarizedexperiment)))
+    (native-inputs
+     `(("r-knitr" ,r-knitr)))
+    (home-page
+     "https://bioconductor.org/packages/release/bioc/html/FourCSeq.html")
+    (synopsis "Analysis of multiplexed 4C sequencing data")
+    (description
+     "This package is an R package dedicated to the analysis of (multiplexed)
+4C sequencing data.  @code{r-fourcseq} provides a pipeline to detect specific
+interactions between DNA elements and identify differential interactions
+between conditions.  The statistical analysis in R starts with individual bam
+files for each sample as inputs.  To obtain these files, the package contains
+a Python script to demultiplex libraries and trim off primer sequences.  With
+a standard alignment software the required bam files can be then be
+generated.")
+    (license license:gpl3+)))