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: | 0.1.0 |
| Depends: | R (≥ 3.5.0) |
| Imports: | dplyr, ggplot2, ggrepel, graphics, grDevices, igraph, magrittr, Matrix, methods, pROC, parallel, Rcpp, rlang, scales, tibble, utils, uwot, withr |
| LinkingTo: | Rcpp, RcppArmadillo, RcppProgress, RcppEigen |
| Suggests: | ggrastr (≥ 0.1.7), pbapply, rmumps, testthat |
| Published: | 2020-09-30 |
| Author: | Peter Kharchenko [aut], Viktor Petukhov [aut], Ramus Rydbirk [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 |
| CRAN checks: | sccore results |
| Reference manual: | sccore.pdf |
| Package source: | sccore_0.1.0.tar.gz |
| Windows binaries: | r-devel: sccore_0.1.0.zip, r-release: sccore_0.1.0.zip, r-oldrel: sccore_0.1.0.zip |
| macOS binaries: | r-release: not available, r-oldrel: sccore_0.1.0.tgz |
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