GNU bug report logs - #66966
[Patch] gnu: Add r-bcrank, r-bbcanalyzer, r-baynorm, r-bb, r-bayesspace, r-rcppdist, r-bayesknockdown, r-basicstarrseq, r-basics, r-basic4cseq, r-bsgenome-ecoli-ncbi-20080805, r-bags and r-breastcancervdx

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From: Mădălin Ionel Patrașcu
 <madalinionel.patrascu <at> mdc-berlin.de>
To: <66966 <at> debbugs.gnu.org>
Cc: Ricardo Wurmus <rekado <at> elephly.net>
Subject: [bug#66966] [PATCH 09/13] gnu: Add r-bayesspace.
Date: Mon, 6 Nov 2023 12:06:45 +0100

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

Change-Id: Id9c0d23e209bafea5941a1e1f968fab5f1724eab
---
 gnu/packages/bioconductor.scm | 47 +++++++++++++++++++++++++++++++++++
 1 file changed, 47 insertions(+)

diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index 12d9e1b077..11ed82bc58 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22465,6 +22465,53 @@ (define-public r-bayesknockdown
 used for differential expression/2-class data.")
     (license license:gpl3)))
 
+(define-public r-bayesspace
+  (package
+    (name "r-bayesspace")
+    (version "1.12.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (bioconductor-uri "BayesSpace" version))
+       (sha256
+        (base32 "1mqgsylnrvf197cin5zzihjv31bm2q0m5a612ncbglys6n1jd105"))))
+    (properties `((upstream-name . "BayesSpace")))
+    (build-system r-build-system)
+    (propagated-inputs
+     (list r-assertthat
+           r-biocfilecache
+           r-biocsingular
+           r-coda
+           r-dirichletreg
+           r-ggplot2
+           r-matrix
+           r-mclust
+           r-purrr
+           r-rcpp
+           r-rcpparmadillo
+           r-rcppdist
+           r-rcppprogress
+           r-rcurl
+           r-rhdf5
+           r-s4vectors
+           r-scales
+           r-scater
+           r-scran
+           r-singlecellexperiment
+           r-summarizedexperiment
+           r-xgboost))
+    (native-inputs (list r-knitr))
+    (home-page "https://www.ezstatconsulting.com/BayesSpace/")
+    (synopsis "Clustering and resolution enhancement of spatial transcriptomes")
+    (description
+     "This package provides tools for clustering and enhancing the resolution of
+spatial gene expression experiments.  BayesSpace clusters a low-dimensional
+representation of the gene expression matrix, incorporating a spatial prior to
+encourage neighboring spots to cluster together.  The method can enhance the
+resolution of the low-dimensional representation into \"sub-spots\", for which
+features such as gene expression or cell type composition can be imputed.")
+    (license license:expat)))
+
 (define-public r-biocthis
   (package
     (name "r-biocthis")
-- 
2.41.0

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