# STrand-specific ANnotation of genomic data

## Documentation for package ‘STAN’ version 1.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

STAN-package | STrand-specific ANnotation of genomic data
.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.
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 | 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.
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_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
yeastTF_SGDGenes | SGD annotation for the yeast TF example