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: | 1.0.6 |
| Depends: | R (≥ 3.5.0) |
| Imports: | dplyr,ggplot2,ggrepel, graphics, grDevices,igraph,irlba,magrittr,Matrix, methods, parallel,pbmcapply,pROC,Rcpp,rlang,scales,Seurat, stats,tibble, utils,uwot,withr |
| LinkingTo: | Rcpp,RcppArmadillo,RcppProgress,RcppEigen |
| Suggests: | ggrastr (≥ 0.1.7),jsonlite,rmumps,testthat |
| Published: | 2025-04-13 |
| 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 |