DEWSeq
Differential Expressed Windows Based on Negative Binomial Distribution
Bioconductor version: Release (3.20)
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 "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, FunctionalGenomics, GeneRegulation, Sequencing, Software |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (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, tidyverse, rmarkdown, testthat, BiocStyle, IHW |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DEWSeq_1.20.0.tar.gz |
| Windows Binary (x86_64) | DEWSeq_1.20.0.zip |
| macOS Binary (x86_64) | DEWSeq_1.20.0.tgz |
| macOS Binary (arm64) | DEWSeq_1.19.0.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 |