STAN

This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.

The Genomic STate ANnotation Package

Bioconductor version: Release (3.17)

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

Installation

To install this package, start R (version "4.3") 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


Reference Manual	PDF

Details

biocViews	ChIPSeq, ChipOnChip, GenomeAnnotation, HiddenMarkovModel, ImmunoOncology, Microarray, RNASeq, Sequencing, Software, Transcription
Version	2.28.0
In Bioconductor since	BioC 3.0 (R-3.1) (9 years)
License	GPL (>= 2)
Depends	methods, poilog, parallel
Imports	GenomicRanges, IRanges, S4Vectors, BiocGenerics, GenomeInfoDb, Gviz, Rsolnp
Linking To
Suggests	BiocStyle, gplots, knitr
System Requirements
Enhances
URL

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
Source Repository	git clone https://git.bioconductor.org/packages/STAN
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/STAN
Package Short Url	https://bioconductor.org/packages/STAN/
Package Downloads Report	Download Stats