REDseq

This package is for version 3.17 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: 3.17

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, Junhui Li and Thomas Fazzio

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

Citation (from within R, enter citation("REDseq")):

Installation

To install this package, start R (version "4.3") and enter:


if (!require("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")
REDseq Vignette PDF R Script
Reference Manual PDF

Details

biocViews Preprocessing, SequenceMatching, Sequencing, Software
Version 1.46.0
In Bioconductor since BioC 2.9 (R-2.14) (12.5 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
System Requirements
URL
See More
Suggests
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 REDseq_1.46.0.tar.gz
Windows Binary REDseq_1.46.0.zip
macOS Binary (x86_64) REDseq_1.46.0.tgz
macOS Binary (arm64) REDseq_1.46.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/REDseq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/REDseq
Bioc Package Browser https://code.bioconductor.org/browse/REDseq/
Package Short Url https://bioconductor.org/packages/REDseq/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.17 Source Archive