bsseq
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see bsseq.
Analyze, manage and store bisulfite sequencing data
Bioconductor version: 3.7
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 "3.5") 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 | 1.16.1 |
| In Bioconductor since | BioC 2.11 (R-2.15) (11.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.3), methods, BiocGenerics, GenomicRanges(>= 1.29.14), SummarizedExperiment(>= 1.9.18), parallel |
| Imports | IRanges(>= 2.11.16), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table, S4Vectors, R.utils (>= 2.0.0), DelayedMatrixStats(>= 1.1.12), permute, limma, DelayedArray(>= 0.5.34), HDF5Array |
| System Requirements | |
| URL | https://github.com/kasperdanielhansen/bsseq |
| Bug Reports | https://github.com/kasperdanielhansen/bsseq/issues |
See More
| Suggests | RUnit, bsseqData, BiocStyle, rmarkdown, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | bsseqData, dmrseq, DSS |
| Imports Me | MIRA, scmeth |
| Suggests Me | tissueTreg |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | bsseq_1.16.1.tar.gz |
| Windows Binary | bsseq_1.16.1.zip |
| Mac OS X 10.11 (El Capitan) | bsseq_1.16.1.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 |
| Old Source Packages for BioC 3.7 | Source Archive |