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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 |
| Reference manual: | sccore.pdf |
| 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 imports: | conos, CRMetrics, leidenAlg, pagoda2, scITD |
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These binaries (installable software) and packages are in development.
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