From f65917f6073b7af9b9249bf225a4ca1ef7f5598b Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 21 Oct 2021 14:34:35 +0000
Subject: gnu: Add r-shaman.

* gnu/packages/bioinformatics.scm (r-shaman): New variable.
---
 gnu/packages/bioinformatics.scm | 44 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 44 insertions(+)

(limited to 'gnu')

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 13ed94c1c2..cd848b6e00 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7734,6 +7734,50 @@ of transcriptional heterogeneity among single cells.")
 analyze genomic data resulting from various experiments.")
     (license license:gpl2)))
 
+(define-public r-shaman
+  (let ((commit "d6944e8ac7bd1dbd5c6cec646eafc1d19d0ca96f")
+        (release "2.0")
+        (revision "2"))
+    (package
+      (name "r-shaman")
+      (version (git-version release revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/tanaylab/shaman")
+                      (commit commit)))
+                (file-name (git-file-name name version))
+                (sha256
+                 (base32
+                  "03sx138dzpfiq23j49z0m0s4j79855mrg64hpj9c83408wzphxi6"))
+                (snippet
+                 ;; This file will be generated.
+                 '(delete-file "inst/doc/shaman-package.R"))))
+      (build-system r-build-system)
+      (propagated-inputs
+       `(("r-data-table" ,r-data-table)
+         ("r-domc" ,r-domc)
+         ("r-ggplot2" ,r-ggplot2)
+         ("r-gviz" ,r-gviz)
+         ("r-misha" ,r-misha)
+         ("r-plyr" ,r-plyr)
+         ("r-rann" ,r-rann)
+         ("r-rcpp" ,r-rcpp)
+         ("r-reshape2" ,r-reshape2)
+         ;; For vignettes
+         ("r-rmarkdown" ,r-rmarkdown)
+         ("r-knitr" ,r-knitr)))
+      (home-page "https://github.com/tanaylab/shaman")
+      (synopsis "Sampling HiC contact matrices for a-parametric normalization")
+      (description "The Shaman package implements functions for
+resampling Hi-C matrices in order to generate expected contact
+distributions given constraints on marginal coverage and
+contact-distance probability distributions.  The package also provides
+support for visualizing normalized matrices and statistical analysis
+of contact distributions around selected landmarks.")
+      ;; Any version of the GPL
+      (license license:gpl3+))))
+
 (define-public r-centipede
   (package
     (name "r-centipede")
-- 
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