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>
License: GPL-3
NeedsCompilation: yes
Materials: README
In views: Omics
CRAN checks: sccore results


Reference manual: sccore.pdf


Package source: sccore_1.0.5.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
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


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