R Observatory: Metrics for craftgrn version 0.1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

craftgrn

0.1.7

Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks

0packages depend

785downloads / year

45.7%test coverage

13/13checks pass

Overview

About

Maintained by Yaoxiang LiFirst published 2026-06-182 releasesCRAN page ↗GitHub ↗

Provides a reproducible framework for constructing and comparing gene regulatory networks by integrating chromatin accessibility footprint scores with matched RNA expression data. It implements context-specific enhancer-gene linking, transcription factor focused network analysis, differential network analysis, and regulatory topic modeling workflows for systematic exploration of gene regulation across conditions. Methodological background is described in Bentsen and others (2020) doi:10.1038/s41467-020-18035-1, Blei, Ng and Jordan (2003) https://www.jmlr.org/papers/v3/blei03a.html, and Chen, Li, Zhu and Chen (2015) doi:10.48550/arXiv.1510.08628.

Install

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

install.packages("craftgrn", 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("oncologylab/craftgrn")

Development version from oncologylab/craftgrn. 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-craftgrn

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-craftgrn

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-craftgrn

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

Health

CRAN checks

13OK

Slowest check: 6.4 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.21

45.7%

Coverage · measured lines

100%

Documentation · exports

19

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
OK2026-06-19
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 810 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 33%
Documented parameters: 98%
Return-value docs: 100%
References docs: 0%

Downloads

785

CRAN downloads in the past year

Rank #12,759 · ~2/day · ~65/mo

Releases R versions

Daily download trend is not available in this view yet.

24130 days

78590 days

7851 year

Compare downloads with other packages →

Also on54 r2u2 autocran

Repository

GitHub ↗ oncologylab/craftgrn

231Stars

0Forks

2Open issues

0Open PRs

1Releases

272Commits

1Contributors

atac-seqbioinformaticschromatin-accessibilitycomputational-biologygene-regulationgene-regulation-networksmultiomicsnetwork-inference

License GPL-3.0 · 272 commits · Last activity 2026-08-13 · +320% stars, 30d

Stars over time

2025-10-31 · 12026-08-18 · 231

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/oncologylab/craftgrn on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

42 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (19)

cliclusterconfig data.table dplyr digest future future.apply ggplot2 enrichR jsonlite LDAvismethodspheatmap readr Rcpp tibble tidyr yaml

LinkingTo (1)

Rcpp

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Yaoxiang Li

Author, Maintainer

Authors (2)

Yaoxiang Li

Author, Maintainer

Chunling Yi

Author

Package Timeline

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

0.1.7Latest
2026-06-20 · current release · diff ↗
0.1.6
2026-06-18
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-18
Total releases: 2 / 1 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 4.1.0
Download size: 764 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("craftgrn")

Format

Li, Y., & Yi, C. (2026). craftgrn: Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks (Version 0.1.7) [Computer software]. https://doi.org/10.32614/CRAN.package.craftgrn

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 craftgrn version 0.1.7 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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