Integrative Chromatin Accessibility and RNA Framework for Gene Regulatory Networks R package craftgrn version 0.1.7 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>. Software 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 Yaoxiang Li <liyaoxiang@outlook.com> Comprehensive R Archive Network (CRAN) Yaoxiang Li [aut, cre], Chunling Yi [aut] GPL (>= 3) 2026-06-19 application/tgz https://CRAN.R-project.org/package=craftgrn doi:10.32614/CRAN.package.craftgrn en-US