diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 129 |
1 files changed, 128 insertions, 1 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 2f2a60ad19..74af02a47d 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -22,6 +22,7 @@ #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) #:use-module (guix download) + #:use-module (guix git-download) #:use-module (guix build-system r) #:use-module (gnu packages) #:use-module (gnu packages base) @@ -37,7 +38,8 @@ #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages statistics) - #:use-module (gnu packages web)) + #:use-module (gnu packages web) + #:use-module (srfi srfi-1)) ;;; Annotations @@ -2263,6 +2265,68 @@ tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.") (license license:artistic2.0))) +(define-public r-monocle3 + (package + (name "r-monocle3") + (version "0.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cole-trapnell-lab/monocle3.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) + (build-system r-build-system) + (propagated-inputs + `(("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-dplyr" ,r-dplyr) + ("r-ggplot2" ,r-ggplot2) + ("r-ggrepel" ,r-ggrepel) + ("r-grr" ,r-grr) + ("r-htmlwidgets" ,r-htmlwidgets) + ("r-igraph" ,r-igraph) + ("r-irlba" ,r-irlba) + ("r-limma" ,r-limma) + ("r-lmtest" ,r-lmtest) + ("r-mass" ,r-mass) + ("r-matrix" ,r-matrix) + ("r-matrix-utils" ,r-matrix-utils) + ("r-pbapply" ,r-pbapply) + ("r-pbmcapply" ,r-pbmcapply) + ("r-pheatmap" ,r-pheatmap) + ("r-plotly" ,r-plotly) + ("r-pryr" ,r-pryr) + ("r-proxy" ,r-proxy) + ("r-pscl" ,r-pscl) + ("r-purrr" ,r-purrr) + ("r-rann" ,r-rann) + ("r-rcpp" ,r-rcpp) + ("r-rcppparallel" ,r-rcppparallel) + ("r-reshape2" ,r-reshape2) + ("r-reticulate" ,r-reticulate) + ("r-rhpcblasctl" ,r-rhpcblasctl) + ("r-rtsne" ,r-rtsne) + ("r-shiny" ,r-shiny) + ("r-slam" ,r-slam) + ("r-spdep" ,r-spdep) + ("r-speedglm" ,r-speedglm) + ("r-stringr" ,r-stringr) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-tibble" ,r-tibble) + ("r-tidyr" ,r-tidyr) + ("r-uwot" ,r-uwot) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/cole-trapnell-lab/monocle3") + (synopsis "Analysis toolkit for single-cell RNA-Seq data") + (description + "Monocle 3 is an analysis toolkit for single-cell RNA-Seq experiments.") + (license license:expat))) + (define-public r-noiseq (package (name "r-noiseq") @@ -5024,3 +5088,66 @@ with separating information will be identified, and these clusters are defined by a sparse number of variables, this method can reduce the complexity of data, to only emphasize the data that actually matters.") (license license:expat))) + +(define-public r-cicero + (package + (name "r-cicero") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "cicero" version)) + (sha256 + (base32 + "0f15l8zrh7l7nnvznb66116hvfk15djb9q240vbscm2w0y5fvkcr")))) + (build-system r-build-system) + (propagated-inputs + `(("r-assertthat" ,r-assertthat) + ("r-biobase" ,r-biobase) + ("r-biocgenerics" ,r-biocgenerics) + ("r-data-table" ,r-data-table) + ("r-dplyr" ,r-dplyr) + ("r-fnn" ,r-fnn) + ("r-genomicranges" ,r-genomicranges) + ("r-ggplot2" ,r-ggplot2) + ("r-glasso" ,r-glasso) + ("r-gviz" ,r-gviz) + ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) + ("r-matrix" ,r-matrix) + ("r-monocle" ,r-monocle) + ("r-plyr" ,r-plyr) + ("r-reshape2" ,r-reshape2) + ("r-s4vectors" ,r-s4vectors) + ("r-stringr" ,r-stringr) + ("r-tibble" ,r-tibble) + ("r-vgam" ,r-vgam))) + (home-page "https://bioconductor.org/packages/cicero/") + (synopsis "Predict cis-co-accessibility from single-cell data") + (description + "Cicero computes putative cis-regulatory maps from single-cell chromatin +accessibility data. It also extends the monocle package for use in chromatin +accessibility data.") + (license license:expat))) + +;; This is the latest commit on the "monocle3" branch. +(define-public r-cicero-monocle3 + (let ((commit "fa2fb6515857a8cfc88bc9af044f34de1bcd2b7b") + (revision "1")) + (package (inherit r-cicero) + (name "r-cicero-monocle3") + (version (git-version "1.3.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cole-trapnell-lab/cicero-release.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "077yza93wdhi08n40md20jwk55k9lw1f3y0063qkk90cpz60wi0c")))) + (propagated-inputs + `(("r-monocle3" ,r-monocle3) + ,@(alist-delete "r-monocle" + (package-propagated-inputs r-cicero))))))) |