To install this package, start R and enter:

## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("STAN")

In most cases, you don't need to download the package archive at all.

STAN

 

STrand-specific ANnotation of genomic data

Bioconductor version: Release (3.1)

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>

Citation (from within R, enter citation("STAN")):

Installation

To install this package, start R and enter:

## try http if https is not available
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")

 

PDF R Script STrand-specific ANnotation of genomic data
PDF   Reference Manual
Text   NEWS

Details

biocViews GenomeAnnotation, HiddenMarkovModel, Microarray, Sequencing, Software
Version 1.2.0
In Bioconductor since BioC 3.0 (R-3.1) (1 year)
License GPL (>= 2)
Depends Rsolnp, methods
Imports
LinkingTo
Suggests BiocStyle, Gviz, GenomicRanges, IRanges, gplots, knitr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Package Source STAN_1.2.0.tar.gz
Windows Binary STAN_1.2.0.zip (32- & 64-bit)
Mac OS X 10.6 (Snow Leopard) STAN_1.2.0.tgz
Mac OS X 10.9 (Mavericks) STAN_1.2.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/STAN/tree/release-3.1
Package Short Url http://bioconductor.org/packages/STAN/
Package Downloads Report Download Stats

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