STAN
This package is for version 3.9 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see STAN.
The Genomic STate ANnotation Package
Bioconductor version: 3.9
Genome segmentation with hidden Markov models has become a useful tool to annotate genomic elements, such as promoters and enhancers. STAN (genomic STate ANnotation) implements (bidirectional) hidden Markov models (HMMs) using a variety of different probability distributions, which can model a wide range of current genomic data (e.g. continuous, discrete, binary). STAN de novo learns and annotates the genome into a given number of 'genomic states'. The 'genomic states' may for instance reflect distinct genome-associated protein complexes (e.g. 'transcription states') or describe recurring patterns of chromatin features (referred to as 'chromatin states'). Unlike other tools, STAN also allows for the integration of strand-specific (e.g. RNA) and non-strand-specific data (e.g. ChIP).
Author: Benedikt Zacher, Julia Ertl, Rafael Campos-Martin, Julien Gagneur, Achim Tresch
Maintainer: Rafael Campos-Martin <campos at mpipz.mpg.de>
citation("STAN")):
Installation
To install this package, start R (version "3.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("STAN")
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("STAN")| The genomic STate ANnotation package | R Script | |
| Reference Manual |
Details
| biocViews | ChIPSeq, ChipOnChip, GenomeAnnotation, HiddenMarkovModel, ImmunoOncology, Microarray, RNASeq, Sequencing, Software, Transcription |
| Version | 2.12.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (9.5 years) |
| License | GPL (>= 2) |
| Depends | methods, poilog, parallel |
| Imports | GenomicRanges, IRanges, S4Vectors, BiocGenerics, GenomeInfoDb, Gviz, Rsolnp |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, gplots, knitr |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | STAN_2.12.0.tar.gz |
| Windows Binary | STAN_2.12.0.zip |
| Mac OS X 10.11 (El Capitan) | STAN_2.12.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/STAN |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/STAN |
| Bioc Package Browser | https://code.bioconductor.org/browse/STAN/ |
| Package Short Url | https://bioconductor.org/packages/STAN/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |