STAN

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see STAN.

STrand-specific ANnotation of genomic data

Bioconductor version: 3.2

STAN (STrand-specic ANnotation of genomic data) implements bidirectional Hidden Markov Models (bdHMM), which are designed for studying directed genomic processes, such as gene transcription, DNA replication, recombination or DNA repair by integrating genomic data. bdHMMs model a sequence of successive observations (e.g. ChIP or RNA measurements along the genome) by a discrete number of 'directed genomic states', which e.g. reflect distinct genome-associated complexes. Unlike standard HMM approaches, bdHMMs allow the integration of strand-specific (e.g. RNA) and non strand-specific data (e.g. ChIP).

Author: Benedikt Zacher, Julien Gagneur, Achim Tresch

Maintainer: Benedikt Zacher <zacher at lmb.uni-muenchen.de>

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("STAN")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("STAN")

Details

Package Archives

Follow Installation instructions to use this package in your R session.