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