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.
STAN-package            STrand-specific ANnotation of genomic data
bdHMM                   Create a bdHMM object
bdHMM-class             This class is a generic container for
                        bidirectional Hidden Markov Models.
bdhmm_ex                Initial bdHMM for the Quick-Start example in
                        the vignette
example                 The data for the Quick-Start example in the
                        vignette
fitHMM                  Fit a Hidden Markov Model
flags                   Pre-computed flag sequence for the Quick-Start
                        example in the vignette
getPosterior            Calculate posterior state distribution.
getViterbi              Calculate the most likely state path
hmm_ex                  Initial HMM for the Quick-Start example in the
                        vignette
humanCD4T_flags_ex      Pre-defined flag sequence for the human
                        CD4T-cell example
humanCD4T_ideogramChr7
                        Ideogram track of human chromosome 7 for the
                        human CD4T-cell example
humanCD4T_initCovs      Pre-computed initial estimates of the
                        covairances for the human CD4T-cell example
humanCD4T_initMeans     Pre-computed initial estimates of the means for
                        the human CD4T-cell example
humanCD4T_probeAnno_ex
                        Genomic positions of processed signal for the
                        human CD4T-cell example
humanCD4T_signal_ex     Processed ChIP-Seq signal for the human
                        CD4T-cell example
humanCD4T_ucscGenes     UCSC gene annotation for the human CD4T-cell
                        example
observations            Observation sequence of the Quick-Start example
                        in the vignette
yeastTF_SGDGenes        SGD annotation for the yeast TF example
yeastTF_databychrom_ex
                        Processed ChIP-on-chip data for yeast TF
                        example
yeastTF_initCovs        Pre-computed initial estimates of the
                        covairances for yeast TF example
yeastTF_initMeans       Pre-computed initial estimates of the means for
                        yeast TF example
yeastTF_probeAnno_ex    Genomic positions of the ChIP-on-chip data for
                        yeast TF example
