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sccore: Core Utilities for Single-Cell RNA-Seq

Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.

Version: 1.0.5
Depends: R (≥ 3.5.0)
Imports: dplyr, ggplot2, ggrepel, graphics, grDevices, igraph, irlba, magrittr, Matrix, methods, parallel, pbmcapply, pROC, Rcpp, rlang, scales, stats, tibble, utils, uwot, withr
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, RcppEigen
Suggests: ggrastr (≥ 0.1.7), jsonlite, rmumps, testthat
Published: 2024-02-23
DOI: 10.32614/CRAN.package.sccore
Author: Viktor Petukhov [aut], Rasmus Rydbirk [aut], Peter Kharchenko [aut], Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt at gmail.com>
BugReports: https://github.com/kharchenkolab/sccore/issues
License: GPL-3
URL: https://github.com/kharchenkolab/sccore
NeedsCompilation: yes
Materials: README
In views: Omics
CRAN checks: sccore results

Documentation:

Reference manual: sccore.pdf

Downloads:

Package source: sccore_1.0.5.tar.gz
Windows binaries: r-devel: sccore_1.0.5.zip, r-release: sccore_1.0.5.zip, r-oldrel: sccore_1.0.5.zip
macOS binaries: r-release (arm64): sccore_1.0.5.tgz, r-oldrel (arm64): sccore_1.0.5.tgz, r-release (x86_64): sccore_1.0.5.tgz, r-oldrel (x86_64): sccore_1.0.5.tgz
Old sources: sccore archive

Reverse dependencies:

Reverse imports: conos, CRMetrics, leidenAlg, pagoda2, scITD

Linking:

Please use the canonical form https://CRAN.R-project.org/package=sccore to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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