BiSeq

DOI: 10.18129/B9.bioc.BiSeq    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see BiSeq.

Processing and analyzing bisulfite sequencing data

Bioconductor version: 3.7

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>

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	1.20.0
In Bioconductor since	BioC 2.12 (R-3.0) (5.5 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
LinkingTo
Suggests
SystemRequirements
Enhances
URL
Depends On Me	RRBSdata
Imports Me	M3D
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	BiSeq_1.20.0.tar.gz
Windows Binary	BiSeq_1.20.0.zip
Mac OS X 10.11 (El Capitan)	BiSeq_1.20.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiSeq
Source Repository (Developer Access)	git clone [email protected]:packages/BiSeq
Package Short Url	http://bioconductor.org/packages/BiSeq/
Package Downloads Report	Download Stats