BiSeq

DOI: 10.18129/B9.bioc.BiSeq    

Processing and analyzing bisulfite sequencing data

Bioconductor version: Release (3.13)

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 gmail.com>

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

Installation

To install this package, start R (version "4.1") 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 1.32.0
In Bioconductor since BioC 2.12 (R-3.0) (8.5 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
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Depends On Me RRBSdata
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Build Report  

Package Archives

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

Source Package BiSeq_1.32.0.tar.gz
Windows Binary BiSeq_1.32.0.zip
macOS 10.13 (High Sierra) BiSeq_1.32.0.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/
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