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).

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("STAN")
AuthorBenedikt Zacher, Julia Ertl, Julien Gagneur, Achim Tresch
Bioconductor views ChIPSeq ChipOnChip GenomeAnnotation HiddenMarkovModel Microarray RNASeq Sequencing Transcription
Date of publicationNone
MaintainerBenedikt Zacher <zacher@genzentrum.lmu.de>
LicenseGPL (>= 2)
Version2.4.0

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

Functions

bdHMM Man page
.bdHMM Man page
[,bdHMM,ANY,ANY,ANY-method Man page
[,bdHMM,ANY,ANY-method Man page
bdHMM-class Man page
binarizeData Man page
c2optimize Man page
call_dpoilog Man page
data2Gviz Man page
DimNames Man page
DirScore Man page
Emission Man page
EmissionParams Man page
example Man page
fitHMM Man page
flags Man page
getAvgSignal Man page
getLogLik Man page
getPosterior Man page
getSizeFactors Man page
getViterbi Man page
HMM Man page
.HMM Man page
[,HMM,ANY,ANY,ANY-method Man page
[,HMM,ANY,ANY-method Man page
HMM-class Man page
HMMEmission Man page
.HMMEmission Man page
HMMEmission-class Man page
initBdHMM Man page
initHMM Man page
InitProb Man page
LogLik Man page
observations Man page
pilot.hg19 Man page
runningMean Man page
STAN-package Man page
StateNames Man page
trainRegions Man page
Transitions Man page
ucscGenes Man page
viterbi2GRanges Man page
viterbi2Gviz Man page
yeastTF_databychrom_ex Man page
yeastTF_SGDGenes Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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