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: 1.0.0
Depends: R (≥ 3.5.0)
Imports: dplyr, ggplot2, ggrepel, graphics, grDevices, igraph, irlba, magrittr, Matrix, methods, parallel, pbmcapply, pROC, Rcpp, rlang, scales, tibble, utils, uwot, withr
LinkingTo: Rcpp, RcppArmadillo, RcppProgress, RcppEigen
Suggests: ggrastr (≥ 0.1.7), rmumps, testthat
Published: 2021-10-07
Author: Viktor Petukhov [aut], Ramus 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
SystemRequirements: C++11
Materials: README
CRAN checks: sccore results

Documentation:

Reference manual: sccore.pdf

Downloads:

Package source: sccore_1.0.0.tar.gz
Windows binaries: r-devel: sccore_1.0.0.zip, r-devel-UCRT: sccore_1.0.0.zip, r-release: sccore_1.0.0.zip, r-oldrel: sccore_1.0.0.zip
macOS binaries: r-release (arm64): sccore_0.1.3.tgz, r-release (x86_64): sccore_1.0.0.tgz, r-oldrel: sccore_1.0.0.tgz
Old sources: sccore archive

Reverse dependencies:

Reverse imports: conos, leidenAlg, pagoda2

Linking:

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