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[bug#55679,2/2] gnu: Add r-scmap.

Message ID 20220527164013.4195-2-madalinionel.patrascu@mdc-berlin.de
State New
Headers show
Series [bug#55679,1/2] gnu: Add r-googlevis. | expand

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Commit Message

Mădălin Ionel Patrașcu May 27, 2022, 4:40 p.m. UTC
* gnu/packages/bioconductor.scm (r-scmap): New variable.
---
 gnu/packages/bioconductor.scm | 41 +++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)
diff mbox series

Patch

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 4baa80dcb1..9c6526331e 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -5049,6 +5049,47 @@  (define-public r-scdblfinder
 comprehensive scDblFinder method.")
     (license license:gpl3)))
 
+(define-public r-scmap
+  (package
+    (name "r-scmap")
+    (version "1.18.0")
+    (source
+      (origin
+        (method url-fetch)
+        (uri (bioconductor-uri "scmap" version))
+        (sha256
+          (base32 "0pfwaa9pgml11b84rpf7afdkmg8kxb4srgpc56571vaz388xrv7l"))))
+    (properties `((upstream-name . "scmap")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-biobase
+           r-biocgenerics
+           r-dplyr
+           r-e1071
+           r-ggplot2
+           r-googlevis
+           r-matrixstats
+           r-proxy
+           r-randomforest
+           r-rcpp
+           r-rcpparmadillo
+           r-reshape2
+           r-s4vectors
+           r-singlecellexperiment
+           r-summarizedexperiment))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/hemberg-lab/scmap")
+    (synopsis "Tool for unsupervised projection of single cell RNA-seq data")
+    (description
+     "@dfn{Single-cell RNA-seq} (scRNA-seq) is widely used to investigate the
+composition of complex tissues since the technology allows researchers to define
+cell-types using unsupervised clustering of the transcriptome.  However, due to
+differences in experimental methods and computational analyses, it is often
+challenging to directly compare the cells identified in two different experiments.
+@code{scmap} is a method for projecting cells from a scRNA-seq experiment onto
+the cell-types or individual cells identified in a different experiment.")
+    (license license:gpl3)))
+
 (define-public r-seqlogo
   (package
     (name "r-seqlogo")