DEWSeq

DOI: 10.18129/B9.bioc.DEWSeq  

This is the development version of DEWSeq; for the stable release version, see DEWSeq.

Differential Expressed Windows Based on Negative Binomial Distribution

Bioconductor version: Development (3.18)

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 "4.3") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("DEWSeq")

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

Documentation

PDF		Reference Manual

Details

biocViews	DifferentialExpression, FunctionalGenomics, GeneRegulation, Sequencing, Software
Version	1.15.0
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
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Build Report

Package Archives

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

Source Package
Windows Binary	DEWSeq_1.15.0.zip
macOS Binary (x86_64)
macOS Binary (arm64)
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