bsseq

This package is for version 3.20 of Bioconductor; for the stable, up-to-date release version, see bsseq.

Analyze, manage and store whole-genome methylation data

Bioconductor version: 3.20

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 iD ORCID: 0000-0003-0086-0687 , Peter Hickey [aut]

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

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

Installation

To install this package, start R (version "4.4") 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 1.42.0

In Bioconductor since BioC 2.11 (R-2.15) (12.5 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, 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

System Requirements

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, beachmat(>= 1.5.2), batchtools

Linking To Rcpp, beachmat

Enhances

Depends On Me biscuiteer, dmrseq, DSS, bsseqData

Imports Me borealis, DMRcate, methylCC, methylSig, MIRA, NanoMethViz, scmeth, SOMNiBUS

Suggests Me methrix, tissueTreg

Links To Me

Build Report Build Report

Package Archives

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

Source Package bsseq_1.42.0.tar.gz

Windows Binary (x86_64) bsseq_1.42.0.zip

macOS Binary (x86_64) bsseq_1.42.0.tgz

macOS Binary (arm64) bsseq_1.42.0.tgz

Source Repository git clone https://git.bioconductor.org/packages/bsseq

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/bsseq

Bioc Package Browser https://code.bioconductor.org/browse/bsseq/

Package Short Url https://bioconductor.org/packages/bsseq/

Package Downloads Report Download Stats