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
