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Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index e890542b31..43f33721df 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+))) |