bsseq

DOI: 10.18129/B9.bioc.bsseq    

Analyze, manage and store bisulfite sequencing data

Bioconductor version: Release (3.13)

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 (version "4.1") and enter:

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

BiocManager::install("bsseq")

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("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	1.28.0
In Bioconductor since	BioC 2.11 (R-2.15) (9 years)
License	Artistic-2.0
Depends	R (>= 4.0), methods, BiocGenerics, GenomicRanges(>= 1.41.5), SummarizedExperiment(>= 1.19.5)
Imports	IRanges(>= 2.23.9), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors(>= 0.27.12), R.utils (>= 2.0.0), DelayedMatrixStats(>= 1.5.2), permute, limma, DelayedArray(>= 0.15.16), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array(>= 1.19.11), rhdf5
LinkingTo	Rcpp, beachmat
Suggests	testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat(>= 1.5.2), BatchJobs
SystemRequirements	C++11
Enhances
URL	https://github.com/kasperdanielhansen/bsseq
BugReports	https://github.com/kasperdanielhansen/bsseq/issues
Depends On Me	biscuiteer, bsseqData, dmrseq, DSS
Imports Me	DMRcate, MethCP, methylCC, methylSig, MIRA, NanoMethViz, scmeth, tcgaWGBSData.hg19
Suggests Me	methrix, tissueTreg
Links To Me
Build Report

Package Archives

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

Source Package	bsseq_1.28.0.tar.gz
Windows Binary	bsseq_1.28.0.zip
macOS 10.13 (High Sierra)	bsseq_1.28.0.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	https://bioconductor.org/packages/bsseq/
Package Downloads Report	Download Stats