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03/03: gnu: Add r-cistopic.
From: |
guix-commits |
Subject: |
03/03: gnu: Add r-cistopic. |
Date: |
Thu, 15 Aug 2019 11:45:22 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit a9815a6cf27dd0e2140038c35d4ad5ef91f6d7d6
Author: Ricardo Wurmus <address@hidden>
Date: Thu Aug 15 17:39:16 2019 +0200
gnu: Add r-cistopic.
* gnu/packages/bioconductor.scm (r-cistopic): New variable.
---
gnu/packages/bioconductor.scm | 44 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 44 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 0a0aee7..ea43bf2 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))))