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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
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 | 1.9.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (2.5 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.4) |
| Imports | GenomicRanges, InteractionSet, plotgardener, S4Vectors, stats, graphics, grDevices, BiocGenerics, Seqinfo, 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_1.9.0.tar.gz |
| Windows Binary (x86_64) | DegCre_1.9.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | DegCre_1.9.0.tgz |
| macOS Binary (sonoma-arm64) | DegCre_1.9.0.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 |