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Probabilistic association of DEGs to CREs from differential data

Bioconductor version: Release (3.19)

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.

Author: Brian S. Roberts [aut, cre]

Maintainer: Brian S. Roberts <brianroberts1976 at>

Citation (from within R, enter citation("DegCre")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

DegCre Introduction and Examples HTML R Script
Reference Manual PDF


biocViews ATACSeq, ChIPSeq, DNaseSeq, GeneExpression, GeneRegulation, RNASeq, Software
Version 1.0.0
In Bioconductor since BioC 3.19 (R-4.4) (< 6 months)
License MIT + file LICENSE
Depends R (>= 4.4)
Imports GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, GenomeInfoDb, IRanges, utils
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Suggests BSgenome, BSgenome.Hsapiens.UCSC.hg38,, BiocStyle, magick, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0)
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Follow Installation instructions to use this package in your R session.

Source Package DegCre_1.0.0.tar.gz
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macOS Binary (x86_64) DegCre_1.0.0.tgz
macOS Binary (arm64) DegCre_1.0.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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