DEWSeq

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

Differential Expressed Windows Based on Negative Binomial Distribution

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DOI: 10.18129/B9.bioc.DEWSeq

Bioconductor version: Development (3.23)

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 "4.6") 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

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 1.25.0

In Bioconductor since BioC 3.10 (R-3.6) (6 years)

License LGPL (>= 3)

Depends R (>= 4.0.0), R.utils, DESeq2, BiocParallel

Imports BiocGenerics, data.table (>= 1.11.8), Seqinfo, 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

Suggests knitr, tidyverse, rmarkdown, testthat, BiocStyle, IHW

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Package Archives

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

Source Package DEWSeq_1.25.0.tar.gz

Windows Binary (x86_64) DEWSeq_1.25.0.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/

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