Package: DegCre
Type: Package
Title: Probabilistic association of DEGs to CREs from differential data
Version: 1.7.0
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: devel
git_last_commit: 97a3d4d
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
