BiSeq

Processing and analyzing bisulfite sequencing data

Bioconductor version: Development (3.0)

The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.

Author: Katja Hebestreit, Hans-Ulrich Klein

Maintainer: Katja Hebestreit <katja.hebestreit at uni-muenster.de>

To install this package, start R and enter:

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

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

    citation("BiSeq")

Documentation

PDF R Script An Introduction to BiSeq
PDF   Reference Manual

Details

biocViews DNAMethylation, Genetics, MethylSeq, Sequencing, Software
Version 1.5.0
In Bioconductor since BioC 2.12 (R-3.0)
License LGPL-3
Depends R (>= 2.15.2), methods, IRanges(>= 1.17.24), GenomicRanges, Formula
Imports methods, BiocGenerics, Biobase, IRanges, GenomicRanges, rtracklayer, parallel, betareg, lokern, Formula, globaltest
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Package Downloads

Package Source BiSeq_1.5.0.tar.gz
Windows Binary BiSeq_1.5.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) BiSeq_1.5.0.tgz
Mac OS X 10.9 (Mavericks)
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