REDseq

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

Bioconductor version: 2.9

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>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("REDseq")

Documentation

PDF R Script REDseq Vignette
PDF   Reference Manual

Details

biocViews Sequencing, SequenceMatching, Preprocessing
Depends R (>= 2.14.0), BSgenome.Celegans.UCSC.ce2, multtest, Biostrings, BSgenome, ChIPpeakAnno
Imports AnnotationDbi, Biostrings, ChIPpeakAnno, graphics, IRanges, multtest, stats, utils
Suggests
System Requirements
License GPL (>=2)
URL
Depends On Me
Imports Me
Suggests Me
Version 1.0.0
Since Bioconductor 2.9 (R-2.14)

Package Downloads

Package Source REDseq_1.0.0.tar.gz
Windows Binary REDseq_1.0.0.zip (32- & 64-bit)
MacOS 10.5 (Leopard) binary REDseq_1.0.0.tgz
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