craftgrn: Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks

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>.

Version:	0.1.7
Depends:	R (≥ 4.1.0)
Imports:	cli, cluster, config, data.table, dplyr, digest, future, future.apply, ggplot2, enrichR, jsonlite, LDAvis, methods, pheatmap, readr, Rcpp, tibble, tidyr, yaml
LinkingTo:	Rcpp
Suggests:	AnnotationDbi, arrow, EnsDb.Hsapiens.v86, EnsDb.Mmusculus.v79, fgsea, golem, ggraph, ggrepel, gtable, gridExtra, htmlwidgets, igraph, Matrix, msigdbr, parallelly, progressr, RColorBrewer, knitr, rmarkdown, rstudioapi, scales, shiny, spelling, testthat, withr
Published:	2026-06-19
DOI:	10.32614/CRAN.package.craftgrn
Author:	Yaoxiang Li [aut, cre], Chunling Yi [aut]
Maintainer:	Yaoxiang Li <liyaoxiang at outlook.com>
BugReports:	https://github.com/oncologylab/craftgrn/issues
License:	GPL (≥ 3)
URL:	https://oncologylab.github.io/craftgrn/, https://github.com/oncologylab/craftgrn
NeedsCompilation:	yes
SystemRequirements:	Optional Shiny app support on Linux may require libuv headers, for example libuv1-dev, or cmake for bundled libuv builds in transitive dependencies.
Language:	en-US
Materials:	README, NEWS
CRAN checks:	craftgrn results

Documentation:

Reference manual:	craftgrn.html , craftgrn.pdf
Vignettes:	Get started with CraftGRN (source, R code)

Downloads:

Package source:	craftgrn_0.1.7.tar.gz
Windows binaries:	r-devel: craftgrn_0.1.7.zip, r-release: craftgrn_0.1.7.zip, r-oldrel: craftgrn_0.1.7.zip
macOS binaries:	r-release (arm64): craftgrn_0.1.7.tgz, r-oldrel (arm64): craftgrn_0.1.7.tgz, r-release (x86_64): craftgrn_0.1.7.tgz, r-oldrel (x86_64): craftgrn_0.1.7.tgz
Old sources:	craftgrn archive

Linking:

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