DEWSeq
This is the released version of DEWSeq; for the devel version, see DEWSeq.
Differential Expressed Windows Based on Negative Binomial Distribution
Bioconductor version: Release (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("DEWSeq")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, FunctionalGenomics, GeneRegulation, Sequencing, Software |
| Version | 1.26.0 |
| In Bioconductor since | BioC 3.10 (R-3.6) (7 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 |
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_1.26.0.tar.gz |
| Windows Binary (x86_64) | DEWSeq_1.26.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | DEWSeq_1.26.0.tgz |
| macOS Binary (sonoma-arm64) | DEWSeq_1.26.0.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 |