R Observatory: Metrics for RaceID version 0.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RaceID

Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data

1packages depend

6.5Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Dominic GrünCRAN page ↗

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).

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("RaceID", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-raceid

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-RaceID

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-RaceID

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘Ltree.Rd’ ‘SCseq.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 13.0 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTE2026-09-08
ERROR10 OK, 2 NOTE, 1 ERROR2026-09-07
NOTE12 OK, 1 NOTE2026-07-11
OK12 OK2026-04-25
NOTE11 OK, 3 NOTE2026-04-22

Show 4 earlier changesHide 4 earlier changes

ERROR10 OK, 3 NOTE, 1 ERROR2026-04-18
NOTE11 OK, 3 NOTE2026-04-10
ERROR10 OK, 3 NOTE, 1 ERROR2026-04-09
NOTE11 OK, 3 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.2

READMENoVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 107includes a package overview page
Examples that run: 93%41 run in a plain check · 3 never run
Exported functions with examples: 42%
Documented parameters: 100%
Return-value docs: 95%
Help pages citing references: 3%

Vignettes (1)

An introduction to RaceID and StemID.

How these are measured

Downloads

6.5K

CRAN downloads in the past year

Rank #5,218 · ~18/day · ~544/mo

Releases R versions

Daily download trend is not available in this view yet.

67730 days

1.6K90 days

6.5K1 year

Compare downloads with other packages →

Also on448 r2u5 autocran7K conda_forge147 bioconda

How downloads are counted

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

Installing RaceID adds 71 packages (44 with compiled code, 53 MB of source tarballs). Heaviest: ggplot2 6.0 MB, harmony 5.1 MB, igraph 4.8 MB.

Depends (1)

R >= 3.5.0

Imports (29)

coopcompilerclusterFateID FNN fpc ggplot2grDevicesharmony ica igraph irlba leiden locfitmethodsMASSMatrixmatrixStatsparallelpheatmap princurve quadprog randomForest runner Rcpp RColorBrewer Rtsne umap vegan

LinkingTo (1)

Rcpp

Suggests (7)

batchelor DESeq2 knitr rmarkdown SingleCellExperiment slingshot SummarizedExperiment

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

sclValid

How these are counted

Code & Tests

Datasets

People & History

People (1)

Dominic Grün

Author, Maintainer since 0.0.9 (2018)

Releases (34)

Pick two releases to compare their code metrics.

0.4.2Latest
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2026-06-16 · current release · diff ↗
unarchivedReturned to CRAN
2026-06-12
0.4.1
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2026-06-12 · diff ↗
archivedRemoved from CRAN
2026-06-11
requires archived package 'harmony'
R
R 4.6.0 released · 2026-04-24
0.4.0
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2026-02-23 · diff ↗
R
R 4.5.0 released · 2025-04-11
0.3.9
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2024-11-24 · diff ↗
0.3.8
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2024-11-05 · diff ↗
0.3.7
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2024-11-02 · diff ↗
0.3.6
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2024-10-26 · diff ↗
R
R 4.4.0 released · 2024-04-24
0.3.5
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2024-04-04 · diff ↗
0.3.4
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2024-01-08 · diff ↗
0.3.3
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2023-09-28 · diff ↗
0.3.2
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2023-08-10 · diff ↗

Show 33 earlier eventsHide 33 earlier events

0.3.1
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2023-07-17 · diff ↗ ·
added 1 export
Seurat2SCseq
R
R 4.3.0 released · 2023-04-21
0.3.0
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2023-03-13 · diff ↗
0.2.9
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2023-03-01 · diff ↗
0.2.8
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2022-11-16 · diff ↗
unarchivedReturned to CRAN
2022-11-01
0.2.7
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2022-11-01 · diff ↗
archivedRemoved from CRAN
2022-10-30
requires archived package 'harmomy'
0.2.6
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2022-08-19 · diff ↗
0.2.5
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2022-08-15 · diff ↗ ·
added 33 exports
calcAlphaG, calcVar, calcVarFit, cleanNN, compTBNoise, corrVar, diffNoisyGenesTB, extractCounts, fitGammaRt, fitLogVarLogMean, fitNBtb, fitNBtbCl, getFilteredCounts, getNode, inspectKNN, maxNoisyGenesTB, plotB, plotDiffNoise, plotExpNoise, plotMV, plotPC, plotPP, plotPT, plotQQ, plotQuantMap, plotUMINoise, plotfeatmap, postfntb, priorfn, pseudoTime and 3 more
0.2.4
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2022-07-19 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
unarchivedReturned to CRAN
2021-04-08
0.2.3
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2021-04-08 · diff ↗
archivedRemoved from CRAN
2021-03-18
requires archived package 'FateID'
0.2.2
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2020-10-08 · diff ↗ ·
added 1 export
compMean
0.2.1
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2020-08-10 · diff ↗
0.2.0
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2020-05-20 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.9
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2020-04-15 · diff ↗
0.1.8
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2020-02-26 · diff ↗
0.1.7
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2020-01-13 · diff ↗
0.1.6
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2019-11-21 · diff ↗
0.1.5
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2019-09-22 · diff ↗
0.1.4
record
2019-09-20 · diff ↗ ·
removed 1 export
plotprojections

added 19 exports
baseLineVar, compNoise, compumap, createKnnMatrix, diffNoisyGenes, fitBackVar, fractDotPlot, getExpData, graphCluster, maxNoisyGenes, noiseBaseFit, plotBackVar, plotNoiseModel, plotPearsonRes, plotRegNB, plotTrProbs, pruneKnn, transitionProbs, updateSC
R
R 3.6.0 released · 2019-04-26
0.1.3
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2019-01-22 · diff ↗
0.1.2
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2018-11-13 · diff ↗
0.1.1
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2018-08-07 · diff ↗
0.1.0
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2018-07-29 · diff ↗
0.0.9
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2018-07-27
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-07-27
Total releases: 34 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 938 KB / 3 files
Download size: 4.7 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("RaceID")

Format

Grün, D. (2026). RaceID: Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data (Version 0.4.2) [Computer software]. https://doi.org/10.32614/CRAN.package.RaceID

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for RaceID version 0.4.2 [Data set]. HJJB, LLC. Data release v2026-10-19. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-19, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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