To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("REDseq")

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

REDseq

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

Bioconductor version: Release (2.14)

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:

source("http://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 1.10.0
In Bioconductor since BioC 2.9 (R-2.14)
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
Suggests
System Requirements
URL
Depends On Me
Imports Me
Suggests Me

Package Archives

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

Package Source REDseq_1.10.0.tar.gz
Windows Binary REDseq_1.10.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) REDseq_1.10.0.tgz
Mac OS X 10.9 (Mavericks) REDseq_1.10.0.tgz
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center