BiSeq

DOI: 10.18129/B9.bioc.BiSeq    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BiSeq.

Processing and analyzing bisulfite sequencing data

Bioconductor version: 3.9

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 (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("BiSeq")

For older versions of R, please refer to the appropriate Bioconductor release.

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	1.24.0
In Bioconductor since	BioC 2.12 (R-3.0) (6.5 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
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URL
Depends On Me	RRBSdata
Imports Me	M3D
Suggests Me
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Build Report

Package Archives

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

Source Package	BiSeq_1.24.0.tar.gz
Windows Binary	BiSeq_1.24.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan)	BiSeq_1.24.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/BiSeq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BiSeq
Package Short Url	https://bioconductor.org/packages/BiSeq/
Package Downloads Report	Download Stats