R Observatory: Metrics for ccRemover version 1.0.4

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ccRemover

1.0.4

Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data

0packages depend

3.5Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Jun LiFirst published 2017-05-184 releasesCRAN page ↗

Implements a method for identifying and removing the cell-cycle effect from scRNA-Seq data. The description of the method is in Barron M. and Li J. (2016) doi:10.1038/srep33892. Identifying and removing the cell-cycle effect from single-cell RNA-Sequencing data. Submitted. Different from previous methods, ccRemover implements a mechanism that formally tests whether a component is cell-cycle related or not, and thus while it often thoroughly removes the cell-cycle effect, it preserves other features/signals of interest in the data.

Install

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

install.packages("ccRemover", 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-ccremover

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-ccRemover

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-ccRemover

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 6.8 min · r-release-macos-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

2

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: not tracked
Return-value docs: not tracked
References docs: 0%

Downloads

3.5K

CRAN downloads in the past year

Rank #16,057 · ~10/day · ~291/mo

Releases R versions

Daily download trend is not available in this view yet.

19330 days

67790 days

3.5K1 year

Compare downloads with other packages →

Also on391 r2u33 autocran1.4K conda_forge

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10.0

Imports (2)

statsutils

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Jun Li

Author, Maintainer

Authors (2)

Jun Li

Author, Maintainer

Martin Barron

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.0.4Latest
2017-08-19 · current release · diff ↗
1.0.3
2017-08-13 · diff ↗
1.0.2
2017-07-26 · diff ↗
1.0.1
2017-05-18
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-05-18
Total releases: 4 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 2.10.0
Bundled data: 1.6 MB / 5 files
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ccRemover")

Format

Li, J., & Barron, M. (2017). ccRemover: Removes the Cell-Cycle Effect from Single-Cell RNA-Sequencing Data (Version 1.0.4) [Computer software]. https://doi.org/10.32614/CRAN.package.ccRemover

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 ccRemover version 1.0.4 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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