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DEWSeq

This package is for version 3.18 of Bioconductor; for the stable, up-to-date release version, see DEWSeq.

Differential Expressed Windows Based on Negative Binomial Distribution


Bioconductor version: 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>

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

Installation

To install this package, start R (version "4.3") 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
NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DifferentialExpression, FunctionalGenomics, GeneRegulation, Sequencing, Software
Version 1.16.2
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, tidyverse, testthat, BiocStyle, IHW
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Package Archives

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

Source Package DEWSeq_1.16.2.tar.gz
Windows Binary DEWSeq_1.16.2.zip (64-bit only)
macOS Binary (x86_64) DEWSeq_1.16.2.tgz
macOS Binary (arm64) DEWSeq_1.16.2.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