From a9815a6cf27dd0e2140038c35d4ad5ef91f6d7d6 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <rekado@elephly.net>
Date: Thu, 15 Aug 2019 17:39:16 +0200
Subject: 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 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))))
-- 
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