bsseq
This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see bsseq.
Analyze, manage and store bisulfite sequencing data
Bioconductor version: 3.11
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 "4.0") 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 | 1.24.4 |
In Bioconductor since | BioC 2.11 (R-2.15) (11.5 years) |
License | Artistic-2.0 |
Depends | R (>= 3.5), methods, BiocGenerics, GenomicRanges(>= 1.33.6), SummarizedExperiment(>= 1.17.4) |
Imports | IRanges(>= 2.22.2), GenomeInfoDb, scales, stats, graphics, Biobase, locfit, gtools, data.table (>= 1.11.8), S4Vectors(>= 0.25.14), R.utils (>= 2.0.0), DelayedMatrixStats(>= 1.5.2), permute, limma, DelayedArray(>= 0.9.8), Rcpp, BiocParallel, BSgenome, Biostrings, utils, HDF5Array(>= 1.11.9), rhdf5 |
System Requirements | C++11 |
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), BatchJobs |
Linking To | Rcpp, beachmat |
Enhances | |
Depends On Me | biscuiteer, bsseqData, dmrseq, DSS |
Imports Me | DMRcate, MethCP, methylCC, methylSig, MIRA, scmeth, tcgaWGBSData.hg19 |
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_1.24.4.tar.gz |
Windows Binary | bsseq_1.24.4.zip (32- & 64-bit) |
macOS 10.13 (High Sierra) | bsseq_1.24.4.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 3.11 | Source Archive |