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 available at <doi:10.1038/s41467-020-18035-1>,
<https://www.jmlr.org/papers/v3/blei03a.html>, and
<doi:10.48550/arXiv.1510.08628>.
| Version: |
0.1.6 |
| 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: |
2026-06-18 |
| DOI: |
10.32614/CRAN.package.craftgrn (may not be active yet) |
| 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 |