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 is the development version of BiSeq; for the stable release version, see BiSeq.

Processing and analyzing bisulfite sequencing data

Bioconductor version: Development (3.4)

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 1.13.0
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, SummarizedExperiment(>= 0.2.0), Formula
Imports methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest
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Package Archives

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

Package Source BiSeq_1.13.0.tar.gz
Windows Binary
Mac OS X 10.9 (Mavericks)
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/BiSeq
Package Short Url http://bioconductor.org/packages/BiSeq/
Package Downloads Report Download Stats

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