bsseq

This is the released version of bsseq; for the devel version, see bsseq.

All versions

3.24 (devel), 3.23 (release), 3.22, 3.21, 3.20, 3.19, 3.18, 3.17, 3.16, 3.15, 3.14, 3.13, 3.12, 3.11, 3.10, 3.9, 3.8, 3.7, 3.6, 3.5, 3.4, 3.3, 3.2, 3.1, 3.0, 2.14, 2.13, 2.12, 2.11

Analyze, manage and store whole-genome methylation data

Bioconductor version: Release (3.23)

A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.

Author: Kasper Daniel Hansen [aut, cre] ORCID: 0000-0003-0086-0687 , Peter Hickey [aut] ORCID: 0000-0002-8153-6258 , Hervé Pagès [ctb], Aaron Lun [ctb]

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

Citation (from within R, enter citation("bsseq")):

Kasper Daniel Hansen, Peter Hickey. bsseq: Analyze, manage and store whole-genome methylation data. doi:10.18129/B9.bioc.bsseq, R package version 1.48.0, https://bioconductor.org/packages/bsseq.

Generated from the package metadata; it may differ from the package's own citation.

Installation

To install this package, start R (version "4.6") and enter:

if (!require("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")

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

Need some help? Ask on the Bioconductor Support site!

Details

biocViews	DNAMethylation, Software
Version	1.48.0
In Bioconductor since	BioC 2.11 (R-2.15) (14 years)
License	Artistic-2.0
Depends	R (>= 4.0), methods, BiocGenerics, GenomicRanges (>= 1.41.5), SummarizedExperiment (>= 1.19.5)
Imports	IRanges (>= 2.23.9), Seqinfo, scales, stats, parallel, tools, 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, beachmat (>= 2.23.2)
System Requirements	C++17
URL	https://github.com/kasperdanielhansen/bsseq
Bug Reports	https://github.com/kasperdanielhansen/bsseq/issues

Suggests	testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, batchtools
Linking To	Rcpp, beachmat, assorthead (>= 1.1.4)
Enhances
Depends On Me	biscuiteer, bsseqData, dmrseq, DSS
Imports Me	borealis, DMRcate, epiSeeker, methodical, methylCC, methylSig, MIRA, NanoMethViz, RBedMethyl, scmeth, SOMNiBUS
Suggests Me	iscream, methFuse, methrix, tissueTreg
Links To Me
Build Report	Build Report, r-universe

Package Archives

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

Source Package	bsseq_1.48.0.tar.gz
Windows Binary (x86_64)	bsseq_1.48.0.zip
macOS Binary (big-sur-x86_64)	bsseq_1.48.0.tgz
macOS Binary (sonoma-arm64)	bsseq_1.48.0.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