To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BiSeq")
In most cases, you don't need to download the package archive at all.
BiSeq
|
This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see BiSeq.
Processing and analyzing bisulfite sequencing data
Bioconductor version: 3.1
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 (from within R,
enter citation("BiSeq")):
Installation
To install this package, start R and enter:
## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("BiSeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("BiSeq")
| R Script | An Introduction to BiSeq | |
| Reference Manual |
Details
| biocViews | DNAMethylation, Genetics, MethylSeq, Sequencing, Software |
| Version | 1.8.0 |
| In Bioconductor since | BioC 2.12 (R-3.0) (3 years) |
| License | LGPL-3 |
| Depends | R (>= 2.15.2), methods, S4Vectors, IRanges(>= 1.17.24), GenomicRanges, Formula |
| Imports | methods, BiocGenerics, Biobase, S4Vectors, IRanges, GenomeInfoDb, GenomicRanges, rtracklayer, parallel, betareg, lokern, Formula, globaltest |
| LinkingTo | |
| Suggests | |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | RRBSdata |
| Imports Me | M3D |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | BiSeq_1.8.0.tar.gz |
| Windows Binary | BiSeq_1.8.0.zip |
| Mac OS X 10.6 (Snow Leopard) | BiSeq_1.8.0.tgz |
| Mac OS X 10.9 (Mavericks) | BiSeq_1.8.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/BiSeq/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/BiSeq/ |
| Package Downloads Report | Download Stats |
Documentation »
Bioconductor
- Package vignettes and manuals.
- Workflows for learning and use.
- Course and conference material.
- Videos.
- Community resources and tutorials.
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations:
- Support site - for questions about Bioconductor packages
- Bioc-devel mailing list - for package developers
