R Observatory: Metrics for craftgrn version 0.1.7

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

craftgrn

0.1.7Package record

Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks

0packages depend

1.7Kdownloads / year

45.7%test coverage

13/13flavors OK

Overview

About

Maintained by Yaoxiang LiCRAN page ↗GitHub ↗Website ↗Issues ↗

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.

Changes in 0.1.7

Updated DESCRIPTION references to include author-year text for the next CRAN update.
Fixed a CRAN macOS test failure by comparing config-resolved relative paths against the canonical project directory path.

From NEWS.md in the release

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. 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-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). 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: 6.1 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-06-19

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.7

READMEYes · 810 wordsVignettesYes · 1 · dynamicNEWSYes · 100% structured · mentions 0.1.7Citation fileNoWebsiteYes · pkgdown

Help pages: 40 (1 internal)
Examples that run: 33%1 run in a plain check · 2 only when donttest examples are enabled (R CMD check --as-cran)
Exported functions with examples: 8%
Documented parameters: 98%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (1)

Get started with CraftGRN HTML

How these are measured

Downloads

1.7K

CRAN downloads in the past year

Rank #7,642 · ~5/day · ~141/mo

Releases R versions

Daily download trend is not available in this view yet.

43930 days

1.1K90 days

1.7K1 year

Compare downloads with other packages →

Also on100 r2u9 autocran

How downloads are counted

Repository

oncologylab/craftgrn ↗Organization: oncologylab

587Stars

3Forks

2Open issues

0Open PRs

1Releases

292Commits

1Commit identities

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

License file reads as GPL-3.0 · 292 commits · Last activity 2026-09-04 · +42.5% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 0
Median days to close, 50 most recently updated closed PRs: 4

Stars over time

2025-10-31 · 12026-10-18 · 587

How these are measured

PracticesBeta

8 development-tooling and community-health practices detected across 6 families in the upstream repository

Checks run against github.com/oncologylab/craftgrn on 2026-10-11.

Continuous integration (1)

GitHub Actions

Governance and community (1)

Code of conduct

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-09-04 · The repository has a site deploy workflow

CRAN release process (1)

cran-comments.md

Show all practicesHide 2 practices

Lint, format, editor (1)

RStudio project

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

42 external dependencies (excludes base and recommended)

Installing craftgrn adds 63 packages (34 with compiled code, 45 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Yaoxiang Li

Author, Maintainer since 0.1.6 (2026)

Chunling Yi

Author

Releases (2)

Pick two releases to compare their code metrics.

0.1.7Latest
record
2026-06-19 · current release · diff ↗
0.1.6
record
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

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 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 craftgrn version 0.1.7 [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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