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: 0.3.5
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: 2024-04-03
DOI: 10.32614/CRAN.package.RaceID
Author: Dominic Grün
Maintainer: Dominic Grün <dominic.gruen at gmail.com>
License: GPL-3
NeedsCompilation: yes
SystemRequirements: C++17
CRAN checks: RaceID results


Reference manual: RaceID.pdf
Vignettes: An introduction to RaceID and StemID.


Package source: RaceID_0.3.5.tar.gz
Windows binaries: r-devel: RaceID_0.3.5.zip, r-release: RaceID_0.3.5.zip, r-oldrel: RaceID_0.3.5.zip
macOS binaries: r-release (arm64): RaceID_0.3.5.tgz, r-oldrel (arm64): RaceID_0.3.5.tgz, r-release (x86_64): RaceID_0.3.5.tgz, r-oldrel (x86_64): RaceID_0.3.5.tgz
Old sources: RaceID archive


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