STAN: The genomic STate ANnotation package

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).

AuthorBenedikt Zacher, Julia Ertl, Julien Gagneur, Achim Tresch
Date of publicationNone
MaintainerBenedikt Zacher <zacher@genzentrum.lmu.de>
LicenseGPL (>= 2)
Version2.2.0

View on Bioconductor

Man pages

bdHMM: Create a bdHMM object

bdHMM-class: This class is a generic container for bidirectional Hidden...

binarizeData: Binarize Sequencing data with the default ChromHMM...

c2optimize: Optimize transitions

call_dpoilog: Calculate density of the Poisson-Log-Normal distribution.

data2Gviz: Convert data for plotting with Gviz

DimNames: Get dimNames of a (bd)HMM

DirScore: Get directionality score of a bdHMM

Emission: Get Emission functions of a (bd)HMM

EmissionParams: Get Emission parameters of a (bd)HMM.

example: The data for the bdHMM example in the vignette and examples...

fitHMM: Fit a Hidden Markov Model

flags: Pre-computed flag sequence for the 'example' data.

getAvgSignal: Compute average signal in state segmentation

getLogLik: Calculate log likelihood state distribution.

getPosterior: Calculate posterior state distribution.

getSizeFactors: Compute size factors

getViterbi: Calculate the most likely state path

HMM: Create a HMM object

HMM-class: This class is a generic container for Hidden Markov Models.

HMMEmission: Create a HMMEmission object

HMMEmission-class: This class is a generic container for different emission...

initBdHMM: Initialization of bidirectional hidden Markov models

initHMM: Initialization of hidden Markov models

InitProb: Get initial state probabilities of a (bd)HMM

LogLik: Get stateNames of a (bd)HMM

observations: Observation sequence for the 'example' data.

pilot.hg19: Genomic positions of processed signal for the Roadmap...

runningMean: Smooth data with running mean

STAN-package: The genomic STate ANnotation package

StateNames: Get stateNames of a (bd)HMM

sub-bdHMM-ANY-ANY-method: This function subsets a bdHMM object. Rows are interpreted as...

sub-HMM-ANY-ANY-method: This function subsets an HMM object. Rows are interpreted as...

trainRegions: Training regions for the Roadmap Epigenomics data set. Three...

Transitions: Get transitions of a (bd)HMM

ucscGenes: UCSC gene annotation for the Roadmap Epigenomics data set.

viterbi2GRanges: Convert the viterbi path to a GRanges object

viterbi2Gviz: Convert state segmentation for plotting with Gviz

yeastTF_databychrom_ex: Processed ChIP-on-chip data for yeast TF example

yeastTF_SGDGenes: SGD annotation for the yeast TF example

Files in this package

STAN/DESCRIPTION
STAN/NAMESPACE
STAN/R
STAN/R/AllClasses.R STAN/R/STAN-package.R STAN/R/bdConstraints.R STAN/R/bdHMMTransMatOptim.R STAN/R/fitHMM.R STAN/R/getLogLik.R STAN/R/getPosterior.R STAN/R/getViterbi.R STAN/R/initBdHMM.R STAN/R/initHMM.R STAN/R/optimizeNB.R STAN/R/optimizePoilog.R STAN/R/utils.R
STAN/build
STAN/build/vignette.rds
STAN/data
STAN/data/example.rda
STAN/data/pilot.hg19.rda
STAN/data/trainRegions.rda
STAN/data/ucscGenes.rda
STAN/data/yeastTF_SGDGenes.rda
STAN/data/yeastTF_databychrom_ex.rda
STAN/inst
STAN/inst/CITATION
STAN/inst/NEWS
STAN/inst/doc
STAN/inst/doc/STAN.R
STAN/inst/doc/STAN.Rnw
STAN/inst/doc/STAN.pdf
STAN/man
STAN/man/DimNames.Rd STAN/man/DirScore.Rd STAN/man/Emission.Rd STAN/man/EmissionParams.Rd STAN/man/HMM-class.Rd STAN/man/HMM.Rd STAN/man/HMMEmission-class.Rd STAN/man/HMMEmission.Rd STAN/man/InitProb.Rd STAN/man/LogLik.Rd STAN/man/STAN-package.Rd STAN/man/StateNames.Rd STAN/man/Transitions.Rd STAN/man/bdHMM-class.Rd STAN/man/bdHMM.Rd STAN/man/binarizeData.Rd STAN/man/c2optimize.Rd STAN/man/call_dpoilog.Rd STAN/man/data2Gviz.Rd STAN/man/example.Rd STAN/man/fitHMM.Rd STAN/man/flags.Rd STAN/man/getAvgSignal.Rd STAN/man/getLogLik.Rd STAN/man/getPosterior.Rd STAN/man/getSizeFactors.Rd STAN/man/getViterbi.Rd STAN/man/initBdHMM.Rd STAN/man/initHMM.Rd STAN/man/observations.Rd STAN/man/pilot.hg19.Rd STAN/man/runningMean.Rd STAN/man/sub-HMM-ANY-ANY-method.Rd STAN/man/sub-bdHMM-ANY-ANY-method.Rd STAN/man/trainRegions.Rd STAN/man/ucscGenes.Rd STAN/man/viterbi2GRanges.Rd STAN/man/viterbi2Gviz.Rd STAN/man/yeastTF_SGDGenes.Rd STAN/man/yeastTF_databychrom_ex.Rd
STAN/src
STAN/src/Bernoulli.cpp
STAN/src/Bernoulli.h
STAN/src/BernoulliFactory.h
STAN/src/DebugConstants.h
STAN/src/EmissionFactory.cpp
STAN/src/EmissionFactory.h
STAN/src/EmissionFunction.cpp
STAN/src/EmissionFunction.h
STAN/src/HMM.cpp
STAN/src/HMM.h
STAN/src/InitialProbability.cpp
STAN/src/InitialProbability.h
STAN/src/JointlyIndependent.cpp
STAN/src/JointlyIndependent.h
STAN/src/JointlyIndependentFactory.h
STAN/src/Makevars
STAN/src/MemoryAllocation.cpp
STAN/src/MemoryAllocation.h
STAN/src/Multinomial.cpp
STAN/src/Multinomial.h
STAN/src/MultinomialFactory.h
STAN/src/MultivariateGaussian.cpp
STAN/src/MultivariateGaussian.h
STAN/src/MultivariateGaussianFactory.h
STAN/src/NegativeBinomial.cpp
STAN/src/NegativeBinomial.h
STAN/src/NegativeBinomialFactory.h
STAN/src/ParamContainerEmissions.cpp
STAN/src/ParamContainerEmissions.h
STAN/src/Poisson.cpp
STAN/src/Poisson.h
STAN/src/PoissonFactory.h
STAN/src/PoissonLogNormal.cpp
STAN/src/PoissonLogNormal.h
STAN/src/PoissonLogNormalFactory.h
STAN/src/RAccessUtils.cpp
STAN/src/RAccessUtils.h
STAN/src/RWrapper.cpp
STAN/src/RWrapper.h
STAN/src/TransitionMatrix.cpp
STAN/src/TransitionMatrix.h
STAN/src/matUtils.cpp
STAN/src/matUtils.h
STAN/vignettes
STAN/vignettes/STAN.Rnw
STAN/vignettes/refs.bib

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