To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("REDseq")

In most cases, you don't need to download the package archive at all.

REDseq

This package is for version 3.0 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: 3.0

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>

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

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("REDseq")

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 1.12.0
In Bioconductor since BioC 2.9 (R-2.14) (4.5 years)
License GPL (>=2)
Depends R (>= 2.15.0), BiocGenerics(>= 0.1.0), BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno
Imports BiocGenerics, AnnotationDbi, Biostrings, ChIPpeakAnno, graphics, IRanges(>= 1.13.5), multtest, stats, utils
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Build Report

Package Archives

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

Package Source REDseq_1.12.0.tar.gz
Windows Binary REDseq_1.12.0.zip
Mac OS X 10.6 (Snow Leopard) REDseq_1.12.0.tgz
Mac OS X 10.9 (Mavericks) REDseq_1.12.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/REDseq/tree/release-3.0
Package Short Url http://bioconductor.org/packages/REDseq/
Package Downloads Report Download Stats

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