Package: craftgrn
Title: Integrative Chromatin Accessibility and RNA Framework for Gene
        Regulatory Networks
Version: 0.1.6
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 available at <doi:10.1038/s41467-020-18035-1>,
    <https://www.jmlr.org/papers/v3/blei03a.html>, and
    <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: 2026-06-11 16:24:12 UTC; yl814
Author: Yaoxiang Li [aut, cre],
  Chunling Yi [aut]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>
Repository: CRAN
Date/Publication: 2026-06-18 16:50:08 UTC
Built: R 4.5.2; aarch64-apple-darwin20; 2026-06-18 20:12:24 UTC; unix
Archs: craftgrn.so.dSYM
