To install this package, start R and enter:

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

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

BiSeq

   

This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see BiSeq.

Processing and analyzing bisulfite sequencing data

Bioconductor version: 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 <katjah at stanford.edu>

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

Installation

To install this package, start R and enter:

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

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("BiSeq")

 

PDF R Script An Introduction to BiSeq
PDF   Reference Manual

Details

biocViews DNAMethylation, Genetics, MethylSeq, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 2.12 (R-3.0) (3 years)
License LGPL-3
Depends R (>= 2.15.2), methods, S4Vectors, IRanges(>= 1.17.24), GenomicRanges, Formula
Imports methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomicRanges, rtracklayer, parallel, betareg, lokern, Formula, globaltest
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me RRBSdata
Imports Me M3D
Suggests Me
Build Report  

Package Archives

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

Package Source BiSeq_1.6.0.tar.gz
Windows Binary BiSeq_1.6.0.zip
Mac OS X 10.6 (Snow Leopard) BiSeq_1.6.0.tgz
Mac OS X 10.9 (Mavericks) BiSeq_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/BiSeq/tree/release-3.0
Package Short Url http://bioconductor.org/packages/BiSeq/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations:

Fred Hutchinson Cancer Research Center