RaceID

0.4.2

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

0packages depend

6.9Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Dominic GrünFirst published 2018-07-2734 releasesCRAN 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.

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).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 10.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-04-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 2 earlier snapshots

ERROR2026-04-09
10 OK · 3 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 93%
Documented parameters: 100%
Return-value docs: 95%
References docs: 3%

Downloads

6.9K

CRAN downloads in the past year

Rank #8,309 · ~19/day · ~578/mo

Releases R versions

Daily download trend is not available in this view yet.

35830 days

1.3K90 days

6.9K1 year

Compare downloads with other packages →

Also on472 r2u37 autocran7K conda_forge117 bioconda

Dependencies

Declared dependencies

30 external dependencies (excludes base and recommended)

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

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Code Composition

R 6,382 (54%)Rd 3,674 (31%)Vignettes 1,473 (12%)C++ 312 (3%)

Code characteristics

Object systems

S4 class2S4 method2

Cyclomatic complexity: 4.0 median / 39 max
System requirements: 1 external

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

164 100 exported

Complexity

7 avg / 39 max

Call network

164 nodes / 116 edges

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (1)

Maintainer (1)

Dominic Grün

Author, Maintainer

Authors (1)

Dominic Grün

Author, Maintainer

Package Timeline

34 releases. Pick two to compare their code metrics. R releases are shown for context.

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

Show 33 earlier events

0.3.1
2023-07-17 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.3.0
2023-03-13 · diff ↗
0.2.9
2023-03-01 · diff ↗
0.2.8
2022-11-16 · diff ↗
0.2.7
2022-11-01 · diff ↗
unarchivedReturned to CRAN
2022-11-01
archivedRemoved from CRAN
2022-10-30
requires archived package 'harmomy'
0.2.6
2022-08-19 · diff ↗
0.2.5
2022-08-15 · diff ↗
0.2.4
2022-07-19 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.2.3
2021-04-08 · diff ↗
unarchivedReturned to CRAN
2021-04-08
archivedRemoved from CRAN
2021-03-18
requires archived package 'FateID'
0.2.2
2020-10-08 · diff ↗
0.2.1
2020-08-10 · diff ↗
0.2.0
2020-05-20 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.9
2020-04-15 · diff ↗
0.1.8
2020-02-26 · diff ↗
0.1.7
2020-01-13 · diff ↗
0.1.6
2019-11-21 · diff ↗
0.1.5
2019-09-22 · diff ↗
0.1.4
2019-09-20 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.1.3
2019-01-22 · diff ↗
0.1.2
2018-11-13 · diff ↗
0.1.1
2018-08-07 · diff ↗
0.1.0
2018-07-29 · diff ↗
0.0.9
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
Installed size: not tracked yet
With dependencies: not tracked yet

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