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Change-Id: I2b0d087378028663ee8d76ced8950f7a9721cb03 --- gnu/packages/bioinformatics.scm | 60 +++++++++++++++++++++++++++++++++ 1 file changed, 60 insertions(+) base-commit: 6341dddcb9e7c8d555ea7294d61dcf64d775e032 diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f574fea0e9..9b45c54ef9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11171,6 +11171,66 @@ (define-public r-archr "This package is designed to streamline scATAC analyses in R.") (license license:gpl2+)))) +(define-public r-azimuth + (let ((commit "243ee5db80fcbffa3452c944254a325a3da2ef9e") + (revision "1")) + (package + (name "r-azimuth") + (version (git-version "0.5.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/satijalab/azimuth") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0vs4813kf2cv2j1z800ihwk62bw4dgmwgkd47rln58581chv39zm")))) + (properties `((upstream-name . "Azimuth"))) + (build-system r-build-system) + (propagated-inputs (list r-bsgenome-hsapiens-ucsc-hg38 + r-dt + r-ensdb-hsapiens-v86 + r-future + r-ggplot2 + r-glmgampoi + r-googlesheets4 + r-hdf5r + r-htmltools + r-httr + r-jaspar2020 + r-jsonlite + r-matrix + r-patchwork + r-plotly + r-presto + r-rcpp + r-rlang + r-scales + r-seurat + r-seuratdata + r-seuratdisk + r-seuratobject + r-shiny + r-shinybs + r-shinydashboard + r-shinyjs + r-signac + r-stringr + r-tfbstools + r-withr)) + (home-page "https://github.com/satijalab/azimuth") + (synopsis + "Shiny app showcasing a single-cell data query-reference mapping algorithm") + (description "Azimuth utilizes an annotated reference dataset. +It automates the processing, analysis, and interpretation. +This applies specifically to new single-cell RNA-seq or +ATAC-seq experiments. Azimuth leverages a reference-based +mapping pipeline that inputs acounts matrix and performs +normalization, visualization, cell annotation, and +differential expression.") + (license license:gpl3)))) + (define-public r-icellnet ;; v1.0 tagged in 2020, last commit contains many fixes. ;; DESCRIPTION says Version: 0.0.0.9000.