Package: epiregulon
Title: Gene regulatory network inference from single cell epigenomic data
Version: 2.1.3
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
git_url: https://git.bioconductor.org/packages/epiregulon
git_branch: devel
git_last_commit: 3a105e9
git_last_commit_date: 2025-12-08
Repository: Bioconductor 3.23
