Package: STAN
Version: 2.2.0
Date: 2016-05-30
Title: The genomic STate ANnotation package
Author: Benedikt Zacher, Julia Ertl, Julien Gagneur, Achim Tresch
Maintainer: Benedikt Zacher <zacher@genzentrum.lmu.de>
Imports: GenomicRanges, IRanges, S4Vectors, BiocGenerics, GenomeInfoDb,
        Gviz, Rsolnp
Depends: methods, poilog, parallel
VignetteBuilder: knitr
Suggests: BiocStyle, gplots, knitr
Description: 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).
License: GPL (>= 2)
biocViews: HiddenMarkovModel, GenomeAnnotation, Microarray, Sequencing,
        ChIPSeq, RNASeq, ChipOnChip, Transcription
LazyLoad: yes
Packaged: 2016-10-18 00:03:16 UTC; biocbuild
NeedsCompilation: yes
Built: R 3.3.1; i386-w64-mingw32; 2016-10-18 04:57:17 UTC; windows
Archs: i386, x64
