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")):

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.

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

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

Suggests knitr, rmarkdown, testthat, BiocStyle, IHW

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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

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Old Source Packages for BioC 3.13 Source Archive