bsseq

DOI: 10.18129/B9.bioc.bsseq    

This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see bsseq.

Analyze, manage and store bisulfite sequencing data

Bioconductor version: 3.7

A collection of tools for analyzing and visualizing bisulfite sequencing data.

Author: Kasper Daniel Hansen [aut, cre], Peter Hickey [aut]

Maintainer: Kasper Daniel Hansen <kasperdanielhansen at gmail.com>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("bsseq")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("bsseq")

 

HTML	R Script	Analyzing WGBS data with bsseq
HTML	R Script	bsseq User's Guide
PDF		Reference Manual
Text		NEWS

Details

biocViews	DNAMethylation, Software
Version	1.16.1
In Bioconductor since	BioC 2.11 (R-2.15) (6 years)
License	Artistic-2.0
Depends	R (>= 3.3), methods, BiocGenerics, GenomicRanges(>= 1.29.14), SummarizedExperiment(>= 1.9.18), parallel
Imports	IRanges(>= 2.11.16), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table, S4Vectors, R.utils (>= 2.0.0), DelayedMatrixStats(>= 1.1.12), permute, limma, DelayedArray(>= 0.5.34), HDF5Array
LinkingTo
Suggests	RUnit, bsseqData, BiocStyle, rmarkdown, knitr
SystemRequirements
Enhances
URL	https://github.com/kasperdanielhansen/bsseq
BugReports	https://github.com/kasperdanielhansen/bsseq/issues
Depends On Me	bsseqData, dmrseq, DSS
Imports Me	MIRA, scmeth
Suggests Me	tissueTreg
Links To Me
Build Report

Package Archives

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

Source Package	bsseq_1.16.1.tar.gz
Windows Binary	bsseq_1.16.1.zip
Mac OS X 10.11 (El Capitan)	bsseq_1.16.1.tgz
Source Repository	git clone https://git.bioconductor.org/packages/bsseq
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/bsseq
Package Short Url	http://bioconductor.org/packages/bsseq/
Package Downloads Report	Download Stats