DegCre

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 yahoo.com>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("DegCre")

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

Documentation

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

browseVignettes("DegCre")

DegCre Introduction and Examples	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Need some help? Ask on the Bioconductor Support site!

Details

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
System Requirements
URL	https://github.com/brianSroberts/DegCre
Bug Reports	https://github.com/brianSroberts/DegCre/issues

Suggests	BSgenome, BSgenome.Hsapiens.UCSC.hg38, org.Hs.eg.db, BiocStyle, magick, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat (>= 3.0.0)
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report	Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	DegCre_1.0.0.tar.gz
Windows Binary (x86_64)	DegCre_1.0.0.zip
macOS Binary (x86_64)	DegCre_1.0.0.tgz
macOS Binary (arm64)	DegCre_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DegCre
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DegCre
Bioc Package Browser	https://code.bioconductor.org/browse/DegCre/
Package Short Url	https://bioconductor.org/packages/DegCre/
Package Downloads Report	Download Stats