Package: RaceID
Title: Identification of Cell Types, Inference of Lineage Trees, and
        Prediction of Noise Dynamics from Single-Cell RNA-Seq Data
Version: 0.4.2
Date: 2026-06-16
Authors@R: person(given = "Dominic",
                    family = "Grün",
                    role = c("aut", "cre"),
                    email = "dominic.gruen@gmail.com")
Maintainer: Dominic Grün <dominic.gruen@gmail.com>
Description: 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>).
Depends: R (>= 3.5.0)
biocViews:
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
VignetteBuilder: knitr
SystemRequirements: C++17
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.2.3
NeedsCompilation: yes
Packaged: 2026-06-16 12:17:59 UTC; d.grun
Author: Dominic Grün [aut, cre]
Repository: CRAN
Date/Publication: 2026-06-16 13:40:02 UTC
Built: R 4.5.3; x86_64-w64-mingw32; 2026-06-24 04:11:49 UTC; windows
Archs: x64
