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311/323: gnu: Add r-catalyst.
From: |
guix-commits |
Subject: |
311/323: gnu: Add r-catalyst. |
Date: |
Mon, 7 Dec 2020 15:14:27 -0500 (EST) |
rekado pushed a commit to branch wip-r
in repository guix.
commit ca7408358948304a119d3557f0cc8ad021ff1b47
Author: zimoun <zimon.toutoune@gmail.com>
AuthorDate: Fri Dec 4 05:16:13 2020 +0100
gnu: Add r-catalyst.
* gnu/packages/bioconductor.scm (r-catalyst): New variable.
---
gnu/packages/bioconductor.scm | 58 +++++++++++++++++++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm
index e890542..43f3372 100644
--- a/gnu/packages/bioconductor.scm
+++ b/gnu/packages/bioconductor.scm
@@ -9140,3 +9140,61 @@ variables.To assure a good level of reproducibility a
post-test filter is
available, where we may set the minimum effect size considered biologicaly
relevant, and the minimum expression of the most abundant condition.")
(license license:gpl2)))
+
+(define-public r-catalyst
+ (package
+ (name "r-catalyst")
+ (version "1.14.0")
+ (source
+ (origin
+ (method url-fetch)
+ (uri (bioconductor-uri "CATALYST" version))
+ (sha256
+ (base32
+ "13af7c4irx1f5yqi32k7kj661vzg32wn3dnps7r9pjijfl4drhrh"))))
+ (properties `((upstream-name . "CATALYST")))
+ (build-system r-build-system)
+ (propagated-inputs
+ `(("r-circlize" ,r-circlize)
+ ("r-complexheatmap" ,r-complexheatmap)
+ ("r-consensusclusterplus" ,r-consensusclusterplus)
+ ("r-cowplot" ,r-cowplot)
+ ("r-data-table" ,r-data-table)
+ ("r-dplyr" ,r-dplyr)
+ ("r-drc" ,r-drc)
+ ("r-flowcore" ,r-flowcore)
+ ("r-flowsom" ,r-flowsom)
+ ("r-ggplot2" ,r-ggplot2)
+ ("r-ggrepel" ,r-ggrepel)
+ ("r-ggridges" ,r-ggridges)
+ ("r-gridextra" ,r-gridextra)
+ ("r-magrittr" ,r-magrittr)
+ ("r-matrix" ,r-matrix)
+ ("r-matrixstats" ,r-matrixstats)
+ ("r-nnls" ,r-nnls)
+ ("r-purrr" ,r-purrr)
+ ("r-rcolorbrewer" ,r-rcolorbrewer)
+ ("r-reshape2" ,r-reshape2)
+ ("r-rtsne" ,r-rtsne)
+ ("r-s4vectors" ,r-s4vectors)
+ ("r-scales" ,r-scales)
+ ("r-scater" ,r-scater)
+ ("r-singlecellexperiment" ,r-singlecellexperiment)
+ ("r-summarizedexperiment" ,r-summarizedexperiment)))
+ (native-inputs
+ `(("r-knitr" ,r-knitr)))
+ (home-page
+ "https://github.com/HelenaLC/CATALYST")
+ (synopsis "Cytometry data analysis tools")
+ (description
+ "This package is Cytometry dATa anALYSis Tools (CATALYST). Mass
+cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as
+reporters to label antibodies, thereby substantially decreasing spectral
+overlap and allowing for examination of over 50 parameters at the single cell
+level. While spectral overlap is significantly less pronounced in CyTOF than
+flow cytometry, spillover due to detection sensitivity, isotopic impurities,
+and oxide formation can impede data interpretability. We designed
+CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for
+preprocessing of cytometry data, including i) normalization using bead
+standards, ii) single-cell deconvolution, and iii) bead-based compensation.")
+ (license license:gpl2+)))
- 250/323: gnu: r-rhtslib: Update to 1.22.0., (continued)
- 250/323: gnu: r-rhtslib: Update to 1.22.0., guix-commits, 2020/12/07
- 265/323: gnu: r-vsn: Update to 3.58.0., guix-commits, 2020/12/07
- 266/323: gnu: r-mzid: Update to 1.28.0., guix-commits, 2020/12/07
- 260/323: gnu: r-protgenerics: Update to 1.22.0., guix-commits, 2020/12/07
- 254/323: gnu: r-tximport: Update to 1.18.0., guix-commits, 2020/12/07
- 262/323: gnu: r-mzr: Fix linking., guix-commits, 2020/12/07
- 280/323: gnu: r-dirichletmultinomial: Update to 1.32.0., guix-commits, 2020/12/07
- 274/323: gnu: r-annotationhub: Update to 2.22.0., guix-commits, 2020/12/07
- 283/323: gnu: r-biovizbase: Update to 1.38.0., guix-commits, 2020/12/07
- 284/323: gnu: r-ggbio: Update to 1.38.0., guix-commits, 2020/12/07
- 311/323: gnu: Add r-catalyst.,
guix-commits <=
- 125/323: gnu: r-rqc: Update to 1.24.0., guix-commits, 2020/12/07
- 126/323: gnu: r-birewire: Update to 3.22.0., guix-commits, 2020/12/07
- 134/323: gnu: r-cytolib: Update to 2.2.0., guix-commits, 2020/12/07
- 140/323: gnu: r-rprotobuflib: Update to 2.2.0., guix-commits, 2020/12/07
- 141/323: gnu: Add r-aws-signature., guix-commits, 2020/12/07
- 150/323: gnu: r-rcistarget: Update to 1.10.0., guix-commits, 2020/12/07
- 160/323: gnu: r-variancepartition: Update to 1.20.0., guix-commits, 2020/12/07
- 165/323: gnu: r-bhc: Update to 1.42.0., guix-commits, 2020/12/07
- 186/323: gnu: r-biocpkgtools: Update to 1.8.0., guix-commits, 2020/12/07
- 191/323: gnu: r-rgreat: Update to 1.22.0., guix-commits, 2020/12/07