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:

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