DegCre
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 (3.21)
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] (ORCID:
Maintainer: Brian S. Roberts <brianroberts1976 at yahoo.com>
citation("DegCre")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4) |
| Imports | GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, GenomeInfoDb, IRanges, BiocParallel, qvalue, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, 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, BiocStyle, magick, knitr, rmarkdown, 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_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | DegCre_1.3.0.tgz |
| macOS Binary (arm64) | DegCre_1.3.0.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 |