DEWSeq

DOI: 10.18129/B9.bioc.DEWSeq  

Differential Expressed Windows Based on Negative Binomial Distribution

Bioconductor version: Release (3.16)

DEWSeq is a sliding window approach for the analysis of differentially enriched binding regions eCLIP or iCLIP next generation sequencing data.

Author: Sudeep Sahadevan [aut], Thomas Schwarzl [aut], bioinformatics team Hentze [aut, cre]

Maintainer: bioinformatics team Hentze <biohentze at embl.de>

Installation

To install this package, start R (version "4.2") and enter:

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

BiocManager::install("DEWSeq")

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("DEWSeq")

 

HTML	R Script	Analyzing eCLIP/iCLIP data with DEWSeq
PDF		Reference Manual
Text		NEWS

Details

biocViews	DifferentialExpression, FunctionalGenomics, GeneRegulation, Sequencing, Software
Version	1.12.0
In Bioconductor since	BioC 3.10 (R-3.6) (3.5 years)
License	LGPL (>= 3)
Depends	R (>= 4.0.0), R.utils, DESeq2, BiocParallel
Imports	BiocGenerics, data.table (>= 1.11.8), GenomeInfoDb, GenomicRanges, methods, S4Vectors, SummarizedExperiment, stats, utils
LinkingTo
Suggests	knitr, rmarkdown, testthat, BiocStyle, IHW
SystemRequirements
Enhances
URL	https://github.com/EMBL-Hentze-group/DEWSeq/
BugReports	https://github.com/EMBL-Hentze-group/DEWSeq/issues
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	DEWSeq_1.12.0.tar.gz
Windows Binary	DEWSeq_1.12.0.zip
macOS Binary (x86_64)	DEWSeq_1.12.0.tgz
macOS Binary (arm64)	DEWSeq_1.12.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/DEWSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/DEWSeq
Bioc Package Browser	https://code.bioconductor.org/browse/DEWSeq/
Package Short Url	https://bioconductor.org/packages/DEWSeq/
Package Downloads Report	Download Stats