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bsseq

Analyze, manage and store bisulfite sequencing data


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") 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

Details

biocViews DNAMethylation, Software
Version 1.38.0
In Bioconductor since BioC 2.11 (R-2.15) (11.5 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, 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
See More
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, bsseqData, dmrseq, DSS
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_1.38.0.tar.gz
Windows Binary bsseq_1.38.0.zip
macOS Binary (x86_64) bsseq_1.38.0.tgz
macOS Binary (arm64) bsseq_1.38.0.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