bsseq

DOI: 10.18129/B9.bioc.bsseq    

This is the development version of bsseq; for the stable release version, see bsseq.

Analyze, manage and store bisulfite sequencing data

Bioconductor version: Development (3.9)

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 "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("bsseq", version = "3.9")

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 1.19.1
In Bioconductor since BioC 2.11 (R-2.15) (6 years)
License Artistic-2.0
Depends R (>= 3.5), methods, BiocGenerics, GenomicRanges(>= 1.29.14), SummarizedExperiment(>= 1.9.18)
Imports IRanges(>= 2.11.16), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors, R.utils (>= 2.0.0), DelayedMatrixStats(>= 1.3.6), permute, limma, DelayedArray(>= 0.7.15), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array(>= 1.11.9), rhdf5
LinkingTo Rcpp, Rhdf5lib, beachmat
Suggests testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat
SystemRequirements C++11
Enhances
URL https://github.com/kasperdanielhansen/bsseq
BugReports https://github.com/kasperdanielhansen/bsseq/issues
Depends On Me bsseqData, dmrseq, DSS
Imports Me MIRA, scmeth, tcgaWGBSData.hg19
Suggests Me tissueTreg
Links To Me
Build Report  

Package Archives

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

Source Package bsseq_1.19.1.tar.gz
Windows Binary bsseq_1.19.1.zip
Mac OS X 10.11 (El Capitan) bsseq_1.19.1.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

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