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:	0.3.9
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:	2024-11-24
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:

Reference manual:	RaceID.pdf
Vignettes:	An introduction to RaceID and StemID. (source, R code)

Downloads:

Package source:	RaceID_0.3.9.tar.gz
Windows binaries:	r-devel: RaceID_0.3.9.zip, r-release: RaceID_0.3.9.zip, r-oldrel: RaceID_0.3.9.zip
macOS binaries:	r-release (arm64): RaceID_0.3.9.tgz, r-oldrel (arm64): RaceID_0.3.9.tgz, r-release (x86_64): RaceID_0.3.9.tgz, r-oldrel (x86_64): RaceID_0.3.9.tgz
Old sources:	RaceID archive

Linking:

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