Package: craftgrn
Title: Integrative Chromatin Accessibility and RNA Framework for Gene
        Regulatory Networks
Version: 0.1.7
Authors@R: c(
    person("Yaoxiang", "Li", , "liyaoxiang@outlook.com", role = c("aut", "cre")),
    person("Chunling", "Yi", role = "aut")
  )
Description: 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>.
License: GPL (>= 3)
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
VignetteBuilder: knitr
SystemRequirements: Optional Shiny app support on Linux may require
        libuv headers, for example libuv1-dev, or cmake for bundled
        libuv builds in transitive dependencies.
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
RoxygenNote: 7.3.3
URL: https://oncologylab.github.io/craftgrn/,
        https://github.com/oncologylab/craftgrn
BugReports: https://github.com/oncologylab/craftgrn/issues
Config/Needs/website: r-lib/pkgdown, tidyverse/tidytemplate
NeedsCompilation: yes
Packaged: 2026-06-19 16:01:05 UTC; yl814
Author: Yaoxiang Li [aut, cre],
  Chunling Yi [aut]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Repository: CRAN
Date/Publication: 2026-06-19 19:40:11 UTC
Built: R 4.7.0; x86_64-w64-mingw32; 2026-07-10 03:58:34 UTC; windows
Archs: x64
