RaceID: Identification of Cell Types, Inference of Lineage Trees, and
Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
Application of 'RaceID' allows inference of cell types and prediction of lineage trees by the 'StemID2' algorithm (Herman, J.S., Sagar, Grun D. (2018) <doi:10.1038/nmeth.4662>). 'VarID2' is part of this package and allows quantification of biological gene expression noise at single-cell resolution (Rosales-Alvarez, R.E., Rettkowski, J., Herman, J.S., Dumbovic, G., Cabezas-Wallscheid, N., Grun, D. (2023) <doi:10.1186/s13059-023-02974-1>).
| Version: |
0.3.7 |
| Depends: |
R (≥ 3.5.0) |
| Imports: |
coop, compiler, cluster, FateID, FNN, fpc, ggplot2, grDevices, harmony, ica, igraph, irlba, leiden, locfit, methods, MASS, Matrix, matrixStats, parallel, pheatmap, princurve, quadprog, randomForest, runner, Rcpp, RColorBrewer, Rtsne, umap, vegan |
| LinkingTo: |
Rcpp (≥ 0.11.0) |
| Suggests: |
batchelor, DESeq2, knitr, rmarkdown, SingleCellExperiment, slingshot, SummarizedExperiment |
| Published: |
2024-11-01 |
| DOI: |
10.32614/CRAN.package.RaceID |
| Author: |
Dominic Grün [aut, cre] |
| Maintainer: |
Dominic Grün <dominic.gruen at gmail.com> |
| License: |
GPL-3 |
| NeedsCompilation: |
yes |
| SystemRequirements: |
C++17 |
| CRAN checks: |
RaceID results |
Documentation:
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