BiSeq

This package is for version 3.21 of Bioconductor; for the stable, up-to-date release version, see BiSeq.

Processing and analyzing bisulfite sequencing data

Bioconductor version: 3.21

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 "4.5") and enter:


if (!require("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")

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 1.48.1

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, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest

System Requirements

URL

Suggests

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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_1.48.1.tar.gz

Windows Binary (x86_64) BiSeq_1.48.1.zip

macOS Binary (x86_64) BiSeq_1.48.1.tgz

macOS Binary (arm64) BiSeq_1.48.1.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

Old Source Packages for BioC 3.21 Source Archive