Package: epiregulon
Title: Gene regulatory network inference from single cell epigenomic
        data
Version: 2.2.0
Date: 2025-12-08
Authors@R: 
    c(person(given = "Xiaosai", family = "Yao", role = c("aut", "cre"), email = "xiaosai.yao@gmail.com", comment = c(ORCID = "0000-0001-9729-0726")),
    person(given = "Tomasz", family = "Włodarczyk", role = c("aut"), email = "tomwlo@gmail.com", comment = c(ORCID = "0000-0003-1554-9699")),
    person(given = "Aaron", family = "Lun", role=c("aut"), email="infinite.monkeys.with.keyboards@gmail.com"),
    person(given = "Shang-Yang", family = "Chen", role = "aut", email = "sychen9584@gmail.com"))
Description: Gene regulatory networks model the underlying gene
        regulation hierarchies that drive gene expression and observed
        phenotypes. Epiregulon infers TF activity in single cells by
        constructing a gene regulatory network (regulons). This is
        achieved through integration of scATAC-seq and scRNA-seq data
        and incorporation of public bulk TF ChIP-seq data. Links
        between regulatory elements and their target genes are
        established by computing correlations between chromatin
        accessibility and gene expressions.
License: MIT + file LICENSE
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.3
Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp,
        S4Vectors, SummarizedExperiment, checkmate, entropy, lifecycle,
        methods, scran, scuttle, stats, utils, AnnotationHub,
        GenomeInfoDb, GenomicRanges, BSgenome.Hsapiens.UCSC.hg19,
        BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10,
        motifmatchr, IRanges, scrapper
Depends: R (>= 4.5.0), SingleCellExperiment
Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0),
        coin, scater, scMultiome
LinkingTo: Rcpp
VignetteBuilder: knitr
URL: https://github.com/xiaosaiyao/epiregulon/
biocViews: SingleCell, GeneRegulation,NetworkInference,Network,
        GeneExpression, Transcription, GeneTarget
Config/testthat/edition: 3
BugReports: https://github.com/xiaosaiyao/epiregulon/issues
Config/pak/sysreqs: libglpk-dev make libgsl0-dev libbz2-dev libicu-dev
        liblzma-dev libpng-dev libxml2-dev libssl-dev xz-utils
        zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2026-04-28 13:03:07 UTC
RemoteUrl: https://github.com/bioc/epiregulon
RemoteRef: RELEASE_3_23
RemoteSha: 90785b2698e28a599b6def878a67dbb325bcdc82
NeedsCompilation: yes
Packaged: 2026-04-29 21:15:11 UTC; root
Author: Xiaosai Yao [aut, cre] (ORCID: <https://orcid.org/0000-0001-9729-0726>),
  Tomasz Włodarczyk [aut] (ORCID:
    <https://orcid.org/0000-0003-1554-9699>),
  Aaron Lun [aut],
  Shang-Yang Chen [aut]
Maintainer: Xiaosai Yao <xiaosai.yao@gmail.com>
Built: R 4.6.0; x86_64-w64-mingw32; 2026-04-29 21:38:21 UTC; windows
Archs: x64
