DEWSeq

This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DEWSeq.

Differential Expressed Windows Based on Negative Binomial Distribution


Bioconductor version: 3.10

Differential expression analysis of windows for next-generation sequencing data like eCLIP or iCLIP data.

Author: Sudeep Sahadevan <sahadeva at embl.de>, Thomas Schwarzl <schwarzl at embl.de>

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

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

Installation

To install this package, start R (version "3.6") 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

Details

biocViews DifferentialExpression, FunctionalGenomics, GeneRegulation, Sequencing, Software
Version 1.0.6
In Bioconductor since BioC 3.10 (R-3.6) (4.5 years)
License LGPL (>= 3)
Depends R (>= 3.6.0), 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
Linking To
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Depends On Me
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Build Report Build Report

Package Archives

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

Source Package DEWSeq_1.0.6.tar.gz
Windows Binary DEWSeq_1.0.6.zip
Mac OS X 10.11 (El Capitan) DEWSeq_1.0.6.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 3.10 Source Archive