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BiSeq

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

Processing and analyzing bisulfite sequencing data


Bioconductor version: Development (3.19)

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 "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
An Introduction to BiSeq PDF R Script
Reference Manual PDF

Details

biocViews DNAMethylation, Genetics, MethylSeq, Sequencing, Software
Version 1.43.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License LGPL-3
Depends R (>= 3.5.0), 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.

Source Package BiSeq_1.43.0.tar.gz
Windows Binary BiSeq_1.43.0.zip
macOS Binary (x86_64) BiSeq_1.43.0.tgz
macOS Binary (arm64) BiSeq_1.43.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/BiSeq
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/BiSeq
Bioc Package Browser https://code.bioconductor.org/browse/BiSeq/
Package Short Url https://bioconductor.org/packages/BiSeq/
Package Downloads Report Download Stats