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09/13: gnu: Add r-bayesspace.
From: |
guix-commits |
Subject: |
09/13: gnu: Add r-bayesspace. |
Date: |
Mon, 13 Nov 2023 09:10:06 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit 53b4e01e2947296ed48f584bcfded865fc0f1a75
Author: Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de>
AuthorDate: Mon Nov 6 12:06:45 2023 +0100
gnu: Add r-bayesspace.
* 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 d27ccce6c2..80de46ac2a 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -22781,6 +22781,53 @@ variable is the knocked-down gene, while the other
genes are potential
targets. It can also be 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")
- 06/13: gnu: Add r-basicstarrseq., (continued)
- 06/13: gnu: Add r-basicstarrseq., guix-commits, 2023/11/13
- 08/13: gnu: Add r-rcppdist., guix-commits, 2023/11/13
- 01/13: gnu: Add r-breastcancervdx., guix-commits, 2023/11/13
- 03/13: gnu: Add r-bsgenome-ecoli-ncbi-20080805., guix-commits, 2023/11/13
- 04/13: gnu: Add r-basic4cseq., guix-commits, 2023/11/13
- 07/13: gnu: Add r-bayesknockdown., guix-commits, 2023/11/13
- 10/13: gnu: Add r-bb., guix-commits, 2023/11/13
- 13/13: gnu: Add r-bcrank., guix-commits, 2023/11/13
- 12/13: gnu: Add r-bbcanalyzer., guix-commits, 2023/11/13
- 11/13: gnu: Add r-baynorm., guix-commits, 2023/11/13
- 09/13: gnu: Add r-bayesspace.,
guix-commits <=