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("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 | ||
NEWS | Text | |
LICENSE | Text |
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 |
See More
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 | |
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Depends On Me | |
Imports Me | |
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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 | 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 |