Package: epiregulon.extra
Title: Companion package to epiregulon with additional plotting,
        differential and graph functions
Version: 1.9.1
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)
Imports: ComplexHeatmap, Matrix, SummarizedExperiment, circlize,
        clusterProfiler, ggplot2, ggraph, igraph, patchwork, scales,
        scater, S4Vectors, methods, epiregulon
Depends: R (>= 4.4), SingleCellExperiment
Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0),
        msigdbr, scMultiome, scuttle, vdiffr, ggrastr, ggrepel, scran,
        scrapper
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
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libglpk-dev make libgsl0-dev libbz2-dev
        libicu-dev liblzma-dev libpng-dev libuv1-dev libxml2-dev
        libssl-dev perl xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-15 07:44:27 UTC
RemoteUrl: https://github.com/bioc/epiregulon.extra
RemoteRef: HEAD
RemoteSha: 738746fa67643cd1a27a2cc339d41e68b080ce2a
NeedsCompilation: no
Packaged: 2026-07-16 05:35:08 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>),
  Timothy Keyes [aut],
  Shang-Yang Chen [aut]
Maintainer: Xiaosai Yao <xiaosai.yao@gmail.com>
Built: R 4.6.1; ; 2026-07-16 05:54:28 UTC; windows
