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, enrichly,
        future, future.apply, ggplot2, enrichR, jsonlite, methods,
        pheatmap, readr, Rcpp, tibble, tidyr, yaml
LinkingTo: Rcpp
Suggests: AnnotationDbi, arrow, Biobase, clue, EnsDb.Hsapiens.v86,
        EnsDb.Mmusculus.v79, fgsea, FNN, ggrastr, golem, ggraph,
        ggrepel, gtable, gridExtra, htmlwidgets, igraph, Matrix,
        matrixStats, msigdbr, parallelly, progressr, RColorBrewer,
        RUVSeq, limma, knitr, org.Hs.eg.db, org.Mm.eg.db, rmarkdown,
        rstudioapi, scales, shiny, spelling, testthat, uwot, 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
Remotes: oncologylab/enrichly
Config/Needs/website: r-lib/pkgdown, tidyverse/tidytemplate
Config/pak/sysreqs: cmake libicu-dev libuv1-dev libssl-dev perl
        libx11-dev
Repository: https://oncologylab.r-universe.dev
Date/Publication: 2026-09-04 05:40:36 UTC
RemoteUrl: https://github.com/oncologylab/craftgrn
RemoteRef: HEAD
RemoteSha: b905506ec0b574bd30de83f6bc2537565793f6e6
NeedsCompilation: yes
Packaged: 2026-10-04 10:15:15 UTC; root
Author: Yaoxiang Li [aut, cre],
  Chunling Yi [aut]
Maintainer: Yaoxiang Li <liyaoxiang@outlook.com>