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| author | Ricardo Wurmus <rekado@elephly.net> | 2019-08-15 17:39:16 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2019-08-15 17:44:25 +0200 |
| commit | a9815a6cf27dd0e2140038c35d4ad5ef91f6d7d6 (patch) | |
| tree | 21f9faf7873ad948660b03f19294a15e7c4c34d3 /gnu/packages | |
| parent | bb88417fb70f8881d46e2f2e8235a1aa16591a36 (diff) | |
| download | guix-a9815a6cf27dd0e2140038c35d4ad5ef91f6d7d6.tar guix-a9815a6cf27dd0e2140038c35d4ad5ef91f6d7d6.tar.gz | |
gnu: Add r-cistopic.
* gnu/packages/bioconductor.scm (r-cistopic): New variable.
Diffstat (limited to 'gnu/packages')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 44 |
1 files changed, 44 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 0a0aee7309..ea43bf2fdf 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -5186,3 +5186,47 @@ accessibility data.") `(("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)))) |