REDseq

DOI: 10.18129/B9.bioc.REDseq    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see REDseq.

Analysis of high-throughput sequencing data processed by restriction enzyme digestion

Bioconductor version: 3.11

The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.

Author: Lihua Julie Zhu and Thomas Fazzio

Maintainer: Lihua Julie Zhu <julie.zhu at umassmed.edu>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("REDseq")

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("REDseq")

 

PDF	R Script	REDseq Vignette
PDF		Reference Manual

Details

biocViews	Preprocessing, SequenceMatching, Sequencing, Software
Version	1.34.0
In Bioconductor since	BioC 2.9 (R-2.14) (9 years)
License	GPL (>=2)
Depends	R (>= 3.5.0), BiocGenerics, BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno
Imports	AnnotationDbi, graphics, IRanges(>= 1.13.5), stats, utils
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Package Archives

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

Source Package	REDseq_1.34.0.tar.gz
Windows Binary	REDseq_1.34.0.zip
macOS 10.13 (High Sierra)	REDseq_1.34.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/REDseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/REDseq
Package Short Url	https://bioconductor.org/packages/REDseq/
Package Downloads Report	Download Stats