Package: DegCre
Type: Package
Title: Probabilistic association of DEGs to CREs from differential data
Version: 1.6.0
Date: 2025-07-22
Authors@R: c(person(given="Brian S.",
                  family="Roberts",
                  email = "brianroberts1976@yahoo.com",
                  role = c("aut", "cre"),
                  comment=c(ORCID = "0009-0001-2914-6826")))
Maintainer: Brian S. Roberts <brianroberts1976@yahoo.com>
Description: 
    DegCre generates associations between differentially expressed genes (DEGs)
    and cis-regulatory elements (CREs) based on non-parametric concordance 
    between differential data. The user provides GRanges of DEG TSS and CRE 
    regions with differential p-value and optionally log-fold changes and 
    DegCre returns an annotated Hits object with associations and their 
    calculated probabilities. Additionally, the package provides functionality 
    for visualization and conversion to other formats.
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.3.2
Depends: R (>= 4.4)
URL: https://github.com/brianSroberts/DegCre
Imports: GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats,
        graphics, grDevices, BiocGenerics, Seqinfo, IRanges,
        BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene,
        org.Hs.eg.db, utils
biocViews: GeneExpression, GeneRegulation, ATACSeq, ChIPSeq, DNaseSeq,
        RNASeq
Suggests: BSgenome, BSgenome.Hsapiens.UCSC.hg38, BiocStyle, magick,
        knitr, rmarkdown, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat
        (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
BugReports: https://github.com/brianSroberts/DegCre/issues
git_url: https://git.bioconductor.org/packages/DegCre
git_branch: RELEASE_3_22
git_last_commit: b521002
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.22
Date/Publication: 2025-10-29
NeedsCompilation: no
Packaged: 2025-10-30 03:25:14 UTC; biocbuild
Author: Brian S. Roberts [aut, cre] (ORCID:
    <https://orcid.org/0009-0001-2914-6826>)
Built: R 4.5.1; ; 2025-10-30 12:12:26 UTC; unix
