Files in STAN

The Genomic STate ANnotation Package

NAMESPACE

DESCRIPTION

build/vignette.rds

src/TransitionMatrix.cpp

src/EmissionFunction.cpp

src/MultivariateGaussian.cpp

src/InitialProbability.cpp

src/TransitionMatrix.h

src/JointlyIndependent.h

src/Multinomial.cpp

src/ParamContainerEmissions.cpp

src/MultinomialFactory.h

src/MemoryAllocation.h

src/RWrapper.h

src/JointlyIndependent.cpp

src/PoissonFactory.h

src/ParamContainerEmissions.h

src/Bernoulli.h

src/MemoryAllocation.cpp

src/MultivariateGaussian.h

src/Bernoulli.cpp

src/MultivariateGaussianFactory.h

src/EmissionFactory.h

src/PoissonLogNormal.cpp

src/DebugConstants.h

src/matUtils.h

src/EmissionFactory.cpp

src/matUtils.cpp

src/Makevars

src/EmissionFunction.h

src/PoissonLogNormalFactory.h

src/Poisson.cpp

src/RWrapper.cpp

src/HMM.h

src/HMM.cpp

src/RAccessUtils.cpp

src/Poisson.h

src/NegativeBinomial.h

src/BernoulliFactory.h

src/NegativeBinomialFactory.h

src/Multinomial.h

src/RAccessUtils.h

src/JointlyIndependentFactory.h

src/PoissonLogNormal.h

src/InitialProbability.h

src/NegativeBinomial.cpp

data/yeastTF_SGDGenes.rda

data/example.rda

data/ucscGenes.rda

data/yeastTF_databychrom_ex.rda

data/trainRegions.rda

data/pilot.hg19.rda

R/fitHMM.R R/optimizePoilog.R R/getLogLik.R R/STAN-package.R R/utils.R R/optimizeNB.R R/initBdClust.R R/initBdHMM.R R/initHMM.R R/bdHMMTransMatOptim.R R/bdConstraints.R R/AllClasses.R R/getViterbi.R R/getPosterior.R R/fitBdClust.R

vignettes/STAN-knitr.Rnw

vignettes/refs.bib

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

inst/doc/STAN-knitr.Rnw

inst/doc/STAN-knitr.pdf inst/doc/STAN-knitr.R

STAN documentation built on Nov. 8, 2020, 11:11 p.m.