GNU bug report logs - #66966
[Patch] gnu: Add r-bcrank, r-bbcanalyzer, r-baynorm, r-bb, r-bayesspace, r-rcppdist, r-bayesknockdown, r-basicstarrseq, r-basics, r-basic4cseq, r-bsgenome-ecoli-ncbi-20080805, r-bags and r-breastcancervdx

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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [bug#66966] [PATCH 04/13] gnu: Add r-basic4cseq.
Date: Mon, 6 Nov 2023 12:06:40 +0100

* gnu/packages/bioconductor.scm (r-basic4cseq): New variable.

Change-Id: I8a031dc010590a8ef4655633026c9dfac35213c3
---
 gnu/packages/bioconductor.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 40402f798f..737d1ca2de 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22277,6 +22277,37 @@ (define-public r-dir-expiry
 eliminating obsolete caches generated by old versions of packages.")
     (license license:gpl3)))
 
+(define-public r-basic4cseq
+  (package
+    (name "r-basic4cseq")
+    (version "1.38.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "Basic4Cseq" version))
+       (sha256
+        (base32 "1vlrrkg885w77w34m2q8hngr95hhh5bkw9hrzyhnp39igjkcwqx4"))))
+    (properties `((upstream-name . "Basic4Cseq")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biostrings
+           r-bsgenome-ecoli-ncbi-20080805
+           r-catools
+           r-genomicalignments
+           r-genomicranges
+           r-rcircos))
+    (home-page "https://bioconductor.org/packages/Basic4Cseq")
+    (synopsis "Analyzing 4C-seq data")
+    (description
+     "Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and
+subsequent visualization of @acronym{4C-seq, circular chromosome conformation
+capture sequencing} data.  Virtual fragment libraries can be created for any
+BSGenome package, and filter functions for both reads and fragments and basic
+quality controls are included.  Fragment data in the vicinity of the experiment's
+viewpoint can be visualized as a coverage plot based on a running median approach
+and a multi-scale contact profile.")
+    (license license:lgpl3)))
+
 (define-public r-basilisk-utils
   (package
     (name "r-basilisk-utils")
-- 
2.41.0

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