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 |