BiSeq

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

Processing and analyzing bisulfite sequencing data

Platform availability badge Ranking badge Support activity badge Years in BioConductor badge Build results badge Last commit badge Dependency count badge

DOI: 10.18129/B9.bioc.BiSeq

Bioconductor version: Development (3.23)

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 "4.6") 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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews DNAMethylation, Genetics, MethylSeq, Sequencing, Software

Version 1.51.0

In Bioconductor since BioC 2.12 (R-3.0) (12.5 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, Seqinfo, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest

System Requirements

URL

Suggests

Linking To

Enhances

Depends On Me RRBSdata

Imports Me

Suggests Me updateObject

Links To Me

Build Report Build Report

Package Archives

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

Source Package BiSeq_1.51.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

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