bsseq
Analyze, manage and store whole-genome methylation data
Bioconductor version: Release (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] 
, 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 | ||
| NEWS | Text |
Details
| biocViews | DNAMethylation, Software |
| Version | 1.42.0 |
| In Bioconductor since | BioC 2.11 (R-2.15) (12 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 |
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, dmrseq, DSS, bsseqData |
| Imports Me | borealis, DMRcate, methylCC, methylSig, MIRA, NanoMethViz, scmeth |
| 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_1.41.1.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 |