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: |
1.0.1 |
| 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: |
2021-12-12 |
| 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 |