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| STAN-package | The genomic STate ANnotation package |
| .bdHMM | This class is a generic container for bidirectional Hidden Markov Models. |
| .HMM | This class is a generic container for Hidden Markov Models. |
| .HMMEmission | This class is a generic container for different emission functions of Hidden Markov Models. |
| bdHMM | Create a bdHMM object |
| bdHMM-class | This class is a generic container for bidirectional Hidden Markov Models. |
| binarizeData | Binarize Sequencing data with the default ChromHMM binarization |
| 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 in the manual |
| fitBdClust | Fit a bidirectional Clustering |
| 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 functions of Hidden Markov Models. |
| initBdClust | Initialization of bidirectional Clustering |
| 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 Epigenomics data set. Regions from the ENCODE pilot phase. |
| runningMean | Smooth data with running mean |
| StateNames | Get stateNames of a (bd)HMM |
| trainRegions | Training regions for the Roadmap Epigenomics data set. Three ENCODE pilot regions with data from two cell lines. |
| 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 |
| [-method | extract parts of HMM |
| [-method | extract parts of bdHMM |