R Observatory: Metrics for rChEA3 version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rChEA3

1.0.1Package record

R Client for the 'ChEA3' Transcription Factor Enrichment API

0packages depend

3.1Kdownloads / year

85.9%test coverage

13/13flavors OK

Overview

About

Maintained by Christophe TavCRAN page ↗GitHub ↗Website ↗Issues ↗

Interface to the 'ChEA3' transcription factor enrichment API. 'ChEA3' integrates evidence from ChIP-seq, co-expression, and literature resources to prioritize transcription factors regulating a given set of genes. This package provides convenient R functions to query the API, retrieve ranked results across collections (including integrated scores), and standardize output for downstream analysis in R/Bioconductor workflows. See https://maayanlab.cloud/chea3/ or Keenan (2019) doi:10.1093/nar/gkz446 for further details.

Changes in 1.0.1

New features

queryChEA3() gains a url argument so users can target a local or self-hosted ChEA3 instance instead of the public API. Defaults to the public endpoint https://maayanlab.cloud/chea3/api/enrich/.

From NEWS.md in the release

Install

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

install.packages("rChEA3", repos = "https://cloud.r-project.org/")

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ckntav/rChEA3")

Development version from ckntav/rChEA3. Installs pak first if it is not already available.

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-rchea3

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-rChEA3

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-rChEA3

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

13OK

CRAN check page ↗

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-05
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 4 earlier changesHide 4 earlier changes

NOTE12 OK, 1 NOTE2026-06-08
OK14 OK2026-03-31
ERROR13 OK, 1 ERROR2026-03-28
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.1

READMEYes · 572 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 1.0.1Citation fileNoWebsiteYes · pkgdown

Help pages: 7
Examples that run: 29%2 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 100%
Documented parameters: 91%
Return-value docs: 83%
Help pages citing references: 14%

Vignettes (1)

rChEA3

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #9,859 · ~9/day · ~261/mo

Releases R versions

Daily download trend is not available in this view yet.

40830 days

99690 days

3.1K1 year

Compare downloads with other packages →

Also on74 r2u9 autocran

How downloads are counted

Repository

ckntav/rchea3 ↗Account: ckntav

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-05-28

Responsiveness

not measured

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/ckntav/rchea3 on 2026-10-11.

Continuous integration (1)

GitHub Actions

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-05-28 · The repository has a site deploy workflow

pkgdown site last built 2026-05-28

Reproducibility and dev environment (1)

data-raw/

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

14 external dependencies (excludes base and recommended)

Installing rChEA3 adds 36 packages (21 with compiled code, 20 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (1)

R >= 4.1.0

Imports (10)

cli crayon dplyr ggplot2 httr jsonlite lubridate rlang tidyselect writexl

LinkingTo (0)

none

Suggests (4)

knitr readxl rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Christophe Tav

Author, Maintainer since 0.2.0 (2025)

Releases (2)

Pick two releases to compare their code metrics.

1.0.1Latest
record
2026-05-28 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.2.0
record
2025-10-15
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-10-15
Total releases: 2 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 0.2 KB / 1 file
Download size: 1.2 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("rChEA3")

Format

Tav, C. (2026). rChEA3: R Client for the 'ChEA3' Transcription Factor Enrichment API (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.rChEA3

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 rChEA3 version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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