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gnu: Add r-cistopic.

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* gnu/packages/bioconductor.scm (r-cistopic): New variable.
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Ricardo Wurmus 2019-08-15 17:39:16 +02:00
parent bb88417fb7
commit a9815a6cf2
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1 changed files with 44 additions and 0 deletions
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gnu/packages/bioconductor.scm
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@ -5186,3 +5186,47 @@ (define-public r-cicero-monocle3
`(("r-monocle3" ,r-monocle3)
,@(alist-delete "r-monocle"
(package-propagated-inputs r-cicero)))))))
(define-public r-cistopic
(let ((commit "29abd8df9afb60ff27ac3f0a590930debe926950")
(revision "0"))
(package
(name "r-cistopic")
(version (git-version "0.2.1" revision commit))
(source
(origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/aertslab/cisTopic.git")
(commit commit)))
(file-name (git-file-name name version))
(sha256
(base32
"0s8irpsv5d2zcv4ihanvsf1vrpignzliscxnvs4519af3jmx78h8"))))
(build-system r-build-system)
(propagated-inputs
`(("r-aucell" ,r-aucell)
("r-data-table" ,r-data-table)
("r-dplyr" ,r-dplyr)
("r-dosnow" ,r-dosnow)
("r-dt" ,r-dt)
("r-feather" ,r-feather)
("r-fitdistrplus" ,r-fitdistrplus)
("r-genomicranges" ,r-genomicranges)
("r-ggplot2" ,r-ggplot2)
("r-lda" ,r-lda)
("r-matrix" ,r-matrix)
("r-plyr" ,r-plyr)
("r-rcistarget" ,r-rcistarget)
("r-rtracklayer" ,r-rtracklayer)
("r-s4vectors" ,r-s4vectors)))
(home-page "https://github.com/aertslab/cisTopic")
(synopsis "Modelling of cis-regulatory topics from single cell epigenomics data")
(description
"The sparse nature of single cell epigenomics data can be overruled using
probabilistic modelling methods such as @dfn{Latent Dirichlet
Allocation} (LDA). This package allows the probabilistic modelling of
cis-regulatory topics (cisTopics) from single cell epigenomics data, and
includes functionalities to identify cell states based on the contribution of
cisTopics and explore the nature and regulatory proteins driving them.")
(license license:gpl3))))