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DEWSeq

This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see DEWSeq.

Differential Expressed Windows Based on Negative Binomial Distribution


Bioconductor version: 3.13

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>

Citation (from within R, enter citation("DEWSeq")):

Installation

To install this package, start R (version "4.1") 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")
Analyzing eCLIP/iCLIP data with DEWSeq HTML R Script
Reference Manual PDF
README Text
NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, FunctionalGenomics, GeneRegulation, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 3.10 (R-3.6) (4.5 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
System Requirements
URL https://github.com/EMBL-Hentze-group/DEWSeq/
Bug Reports https://github.com/EMBL-Hentze-group/DEWSeq/issues
See More
Suggests knitr, rmarkdown, testthat, BiocStyle, IHW
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Package Archives

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

Source Package DEWSeq_1.6.0.tar.gz
Windows Binary DEWSeq_1.6.0.zip
macOS 10.13 (High Sierra) DEWSeq_1.6.0.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
Old Source Packages for BioC 3.13 Source Archive