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[bug#55146] gnu: Add r-aggregatebiovar.

Message ID 20220427114436.26482-1-madalinionel.patrascu@mdc-berlin.de
State Accepted
Headers show
Series [bug#55146] gnu: Add r-aggregatebiovar. | expand


Context Check Description
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Commit Message

Mădălin Ionel Patrașcu April 27, 2022, 11:44 a.m. UTC
* gnu/packages/bioconductor.scm (r-aggregatebiovar): New variable.
 gnu/packages/bioconductor.scm | 34 ++++++++++++++++++++++++++++++++++
 1 file changed, 34 insertions(+)

base-commit: 4fb6ef6636acd7608889639c1b2e492517256f76


Ricardo Wurmus April 27, 2022, 2:31 p.m. UTC | #1
Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> writes:

> * gnu/packages/bioconductor.scm (r-aggregatebiovar): New variable.

Applied with minor stylistic changes.  Thanks!
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diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 67ee6079c6..8f76324330 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -1664,6 +1664,40 @@  (define-public r-adamgui
 the @code{GFAGpathUi} function.")
     (license license:gpl2+)))
+(define-public r-aggregatebiovar
+  (package
+    (name "r-aggregatebiovar")
+    (version "1.4.0")
+    (source (origin
+              (method url-fetch)
+              (uri (bioconductor-uri "aggregateBioVar" version))
+              (sha256
+               (base32
+                "1wbfp1pf62di6pzxsf36lmzk6y9dllz1n4iv3mhpb1x8cvy4hqqk"))))
+    (properties `((upstream-name . "aggregateBioVar")))
+    (build-system r-build-system)
+    (propagated-inputs (list r-matrix
+                             r-rlang
+                             r-s4vectors
+                             r-singlecellexperiment
+                             r-summarizedexperiment
+                             r-tibble))
+    (native-inputs (list r-knitr))
+    (home-page "https://github.com/jasonratcliff/aggregateBioVar")
+    (synopsis
+     "Differential gene expression analysis for multi-subject scRNA-seq")
+    (description
+     "This package @code{aggregateBioVar} contains tools to summarize single
+cell gene expression profiles at the level of subject for single cell RNA-seq
+data collected from more than one subject (e.g. biological sample or technical
+replicates).  A @code{SingleCellExperiment} object is taken as input and
+converted to a list of @code{SummarizedExperiment} objects, where each list
+element corresponds to an assigned cell type.  The @code{SummarizedExperiment}
+objects contain aggregate gene-by-subject count matrices and inter-subject
+column metadata for individual subjects that can be processed using downstream
+bulk RNA-seq tools.")
+    (license license:gpl3)))
 (define-public r-aneufinder
     (name "r-aneufinder")