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 |