[PATCH] gnu: Add r-bandits.

OpenSubmitted by Mădălin Ionel Patrașcu.
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  • Mădălin Ionel Patrașcu
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Mădălin Ionel Patrașcu wrote on 28 Jun 00:34 +0200
(address . guix-patches@gnu.org)
20220627223403.21840-1-madalinionel.patrascu@mdc-berlin.de
* gnu/packages/bioconductor.scm (r-bandits): New variable.
---
gnu/packages/bioconductor.scm | 38 +++++++++++++++++++++++++++++++++++
1 file changed, 38 insertions(+)

Toggle diff (53 lines)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 1e87b190c2..628eaacb6c 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -2029,6 +2029,44 @@ (define-public r-aneufinder
 sequencing data.")
     (license license:artistic2.0)))
 
+(define-public r-bandits
+  (package
+    (name "r-bandits")
+    (version "1.12.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "BANDITS" version))
+              (sha256
+               (base32
+                "1423djb7cij68y0q2dcp8q7lrcn2fxjn6d25v4qy3w00b2w8ppg9"))))
+    (properties `((upstream-name . "BANDITS")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biocparallel
+           r-data-table
+           r-doparallel
+           r-dorng
+           r-drimseq
+           r-foreach
+           r-ggplot2
+           r-mass
+           r-r-utils
+           r-rcpp
+           r-rcpparmadillo))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/SimoneTiberi/BANDITS")
+    (synopsis "Bayesian analysis of differential splicing")
+    (description
+     "@code{BANDITS} is a Bayesian hierarchical model for detecting differential
+splicing of genes and transcripts, via @dfn{DTU} (differential transcript usage),
+between two or more conditions.  The method uses a Bayesian hierarchical framework,
+which allows for sample specific proportions in a Dirichlet-Multinomial model,
+and samples the allocation of fragments to the transcripts.  Parameters are
+inferred via @dfn{MCMC} (Markov chain Monte Carlo) techniques and a DTU test is
+performed via a multivariate Wald test on the posterior densities for the average
+relative abundance of transcripts.")
+    (license license:gpl3+)))
+
 (define-public r-biocversion
   (package
     (name "r-biocversion")

base-commit: 144a750f8b10e606751bc887bcb09e7fb7ae09ff
-- 
2.36.1
?