BiSeq
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BiSeq.
Processing and analyzing bisulfite sequencing data
Bioconductor version: 3.9
The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.
Author: Katja Hebestreit, Hans-Ulrich Klein
Maintainer: Katja Hebestreit <katjah at stanford.edu>
citation("BiSeq")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("BiSeq")
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("BiSeq")| An Introduction to BiSeq | R Script | |
| Reference Manual |
Details
| biocViews | DNAMethylation, Genetics, MethylSeq, Sequencing, Software |
| Version | 1.24.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (11 years) |
| License | LGPL-3 |
| Depends | R (>= 2.15.2), methods, S4Vectors, IRanges(>= 1.17.24), GenomicRanges, SummarizedExperiment(>= 0.2.0), Formula |
| Imports | methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, SummarizedExperiment, rtracklayer, parallel, betareg, lokern, Formula, globaltest |
| System Requirements | |
| URL |
See More
| Suggests | |
| Linking To | |
| Enhances | |
| Depends On Me | RRBSdata |
| Imports Me | M3D |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BiSeq_1.24.0.tar.gz |
| Windows Binary | BiSeq_1.24.0.zip (32- & 64-bit) |
| Mac OS X 10.11 (El Capitan) | BiSeq_1.24.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/BiSeq |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/BiSeq |
| Bioc Package Browser | https://code.bioconductor.org/browse/BiSeq/ |
| Package Short Url | https://bioconductor.org/packages/BiSeq/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |