Package: epiregulon
Title: Gene regulatory network inference from single cell epigenomic
        data
Version: 1.4.0
Date: 2025-03-03
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: 7.3.2
Imports: AnnotationHub, BiocParallel, ExperimentHub, Matrix, Rcpp,
        S4Vectors, SummarizedExperiment, bluster, checkmate, entropy,
        lifecycle, methods, scran, scuttle, stats, utils, scMultiome,
        GenomeInfoDb, GenomicRanges, AUCell,
        BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg38,
        BSgenome.Mmusculus.UCSC.mm10, motifmatchr, IRanges, beachmat
Depends: R (>= 4.4), SingleCellExperiment
Suggests: knitr, rmarkdown, parallel, BiocStyle, testthat (>= 3.0.0),
        coin, scater, beachmat.hdf5
LinkingTo: Rcpp, beachmat, assorthead
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: RELEASE_3_21
git_last_commit: 48ac888
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.21
Date/Publication: 2025-04-15
NeedsCompilation: yes
Packaged: 2025-04-16 00:37:09 UTC; biocbuild
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 4.5.0; x86_64-w64-mingw32; 2025-04-16 14:24:50 UTC; windows
Archs: x64
