Mădălin Ionel Patrașcu wrote 3 years ago
(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