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This is the development version of DegCre; for the stable release version, see DegCre.

Probabilistic association of DEGs to CREs from differential data

Bioconductor version: Development (3.20)

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))

# The following initializes usage of Bioc devel


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 1.1.0
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_1.1.0.tar.gz
Windows Binary (64-bit only)
macOS Binary (x86_64) DegCre_1.1.0.tgz
macOS Binary (arm64) DegCre_1.1.0.tgz
Source Repository git clone
Source Repository (Developer Access) git clone
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