diff options
Diffstat (limited to 'gnu/packages/bioconductor.scm')
| -rw-r--r-- | gnu/packages/bioconductor.scm | 118 |
1 files changed, 115 insertions, 3 deletions
diff --git a/gnu/packages/bioconductor.scm b/gnu/packages/bioconductor.scm index 35fb43b3cd..e8d353f49a 100644 --- a/gnu/packages/bioconductor.scm +++ b/gnu/packages/bioconductor.scm @@ -6205,6 +6205,80 @@ classification (assignment) methods. It also contains a Shiny application for interactive exploration of results.") (license license:gpl2+))) +(define-public r-residualmatrix + (package + (name "r-residualmatrix") + (version "1.2.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "ResidualMatrix" version)) + (sha256 + (base32 + "0p7va19aw0j6anx7ck879kbi5cn7dy712h5ia94adr38ssismv1v")))) + (properties + `((upstream-name . "ResidualMatrix"))) + (build-system r-build-system) + (propagated-inputs + `(("r-delayedarray" ,r-delayedarray) + ("r-matrix" ,r-matrix) + ("r-s4vectors" ,r-s4vectors))) + (native-inputs + `(("r-knitr" ,r-knitr))) + (home-page "https://github.com/LTLA/ResidualMatrix") + (synopsis "Create a DelayedMatrix of regression residuals") + (description + "This package implements tools for delayed computation of a matrix of +residuals after fitting a linear model to each column of an input matrix. It +also supports partial computation of residuals where selected factors are to +be preserved in the output matrix. It implements a number of efficient +methods for operating on the delayed matrix of residuals, most notably matrix +multiplication and calculation of row/column sums or means.") + (license license:gpl3))) + +(define-public r-batchelor + (package + (name "r-batchelor") + (version "1.8.0") + (source + (origin + (method url-fetch) + (uri (bioconductor-uri "batchelor" version)) + (sha256 + (base32 + "1xm204wp3m3mmlc1s59lscbbjvwm5nj32vvf16njcg7pb32lsiqa")))) + (properties `((upstream-name . "batchelor"))) + (build-system r-build-system) + (propagated-inputs + `(("r-beachmat" ,r-beachmat) + ("r-biocgenerics" ,r-biocgenerics) + ("r-biocneighbors" ,r-biocneighbors) + ("r-biocparallel" ,r-biocparallel) + ("r-biocsingular" ,r-biocsingular) + ("r-delayedarray" ,r-delayedarray) + ("r-delayedmatrixstats" ,r-delayedmatrixstats) + ("r-igraph" ,r-igraph) + ("r-matrix" ,r-matrix) + ("r-rcpp" ,r-rcpp) + ("r-residualmatrix" ,r-residualmatrix) + ("r-s4vectors" ,r-s4vectors) + ("r-scaledmatrix" ,r-scaledmatrix) + ("r-scuttle" ,r-scuttle) + ("r-singlecellexperiment" ,r-singlecellexperiment) + ("r-summarizedexperiment" ,r-summarizedexperiment))) + (native-inputs `(("r-knitr" ,r-knitr))) + (home-page "https://bioconductor.org/packages/batchelor") + (synopsis "Single-Cell Batch Correction Methods") + (description + "This package implements a variety of methods for batch correction of +single-cell (RNA sequencing) data. This includes methods based on detecting +mutually nearest neighbors, as well as several efficient variants of linear +regression of the log-expression values. Functions are also provided to +perform global rescaling to remove differences in depth between batches, and +to perform a principal components analysis that is robust to differences in +the numbers of cells across batches.") + (license license:gpl3))) + (define-public r-mast (package (name "r-mast") @@ -6297,10 +6371,44 @@ 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-leidenbase + (let ((commit "430f22af6982cc7d2e6e77f6b0df47bc970dcbce") + (revision "1")) + (package + (name "r-leidenbase") + (version (git-version "0.1.3" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cole-trapnell-lab/leidenbase") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ylqsmdpv4xq6f6ldxvwkhk33a9i1jcgk60zvksk3iplykfzd6c0")))) + (properties `((upstream-name . "leidenbase"))) + (build-system r-build-system) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("gfortran" ,gfortran))) + (propagated-inputs + `(("r-igraph" ,r-igraph))) + (home-page "https://github.com/cole-trapnell-lab/leidenbase") + (synopsis "R and C wrappers to run the Leiden find_partition function") + (description + "This package provides an R to C interface that runs the Leiden +community detection algorithm to find a basic partition. It runs the +equivalent of the @code{find_partition} function. This package includes the +required source code files from the official Leidenalg distribution and +several functions from the R igraph package.") + (license license:gpl3+)))) + (define-public r-monocle3 (package (name "r-monocle3") - (version "0.1.2") + (version "1.0.0") (source (origin (method git-fetch) @@ -6310,10 +6418,12 @@ qPCR data, but could be used with other types as well.") (file-name (git-file-name name version)) (sha256 (base32 - "1cjxqfw3qvy269hsf5v80d4kshl932wrl949iayas02saj6f70ls")))) + "16vpvlbms8fdvpfwzcig0rkg2mxnsq1h80d2l7q3953wm91qc9x4")))) (build-system r-build-system) (propagated-inputs - `(("r-biobase" ,r-biobase) + `(("r-assertthat" ,r-assertthat) + ("r-batchelor" ,r-batchelor) + ("r-biobase" ,r-biobase) ("r-biocgenerics" ,r-biocgenerics) ("r-delayedmatrixstats" ,r-delayedmatrixstats) ("r-dplyr" ,r-dplyr) @@ -6323,6 +6433,7 @@ qPCR data, but could be used with other types as well.") ("r-htmlwidgets" ,r-htmlwidgets) ("r-igraph" ,r-igraph) ("r-irlba" ,r-irlba) + ("r-leidenbase" ,r-leidenbase) ("r-limma" ,r-limma) ("r-lmtest" ,r-lmtest) ("r-mass" ,r-mass) @@ -6342,6 +6453,7 @@ qPCR data, but could be used with other types as well.") ("r-reshape2" ,r-reshape2) ("r-reticulate" ,r-reticulate) ("r-rhpcblasctl" ,r-rhpcblasctl) + ("r-rsample" ,r-rsample) ("r-rtsne" ,r-rtsne) ("r-shiny" ,r-shiny) ("r-slam" ,r-slam) |