Package: DegCre
Type: Package
Title: Probabilistic association of DEGs to CREs from differential data
Version: 1.9.0
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
Config/pak/sysreqs: cmake make libbz2-dev libicu-dev liblzma-dev
        libpng-dev libuv1-dev libxml2-dev libssl-dev xz-utils
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 13:02:34 UTC
RemoteUrl: https://github.com/bioc/DegCre
RemoteRef: HEAD
RemoteSha: 60bbe80337be6932ddd4a3c073c2fa2df8038c61
NeedsCompilation: no
Packaged: 2026-07-14 05:07:24 UTC; root
Author: Brian S. Roberts [aut, cre] (ORCID:
    <https://orcid.org/0009-0001-2914-6826>)