Package: epiregulon.extra
Title: Companion package to epiregulon with additional plotting, differential and graph functions
Version: 1.7.0
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 = "Timothy", family = "Keyes", role=c("aut"), email="keyes.timothy@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: 7.3.2
Imports:
    scran,
    ComplexHeatmap,
    Matrix,
    SummarizedExperiment,
    checkmate,
    circlize,
    clusterProfiler,
    ggplot2,
    ggraph,
    igraph,
    patchwork,
    reshape2,
    scales,
    scater
Depends:
    R (>= 4.4),
    SingleCellExperiment
Suggests:
    epiregulon,
    knitr,
    rmarkdown,
    parallel,
    BiocStyle,
    testthat (>= 3.0.0),
    msigdb,
    GSEABase,
    dorothea,
    scMultiome,
    S4Vectors,
    scuttle,
    vdiffr,
    ggrastr,
    ggrepel
VignetteBuilder: knitr
URL: https://github.com/xiaosaiyao/epiregulon.extra/
biocViews: GeneRegulation, Network, GeneExpression, Transcription, ChipOnChip, DifferentialExpression, GeneTarget, Normalization, GraphAndNetwork
Config/testthat/edition: 3
BugReports: https://github.com/xiaosaiyao/epiregulon.extra/issues
LazyData: true
git_url: https://git.bioconductor.org/packages/epiregulon.extra
git_branch: devel
git_last_commit: a48846b
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
