histoneHMM-package | Analysis of histone modification data using a HMM |
callRegions | call regions from a posterior matrix |
Distribution-class | Class 'Distribution' |
dzinba | Zero inflated negative binomial distribution |
dzinba.copula | Density, CDF and random number generation from a bivariate zinba copula |
em | Expectation maximization algorithm |
EMResult-class | Expectation maximization algorithm |
fit-method | Class 'Distribution' |
fit.zinba.copula | Maximum likelihood fit of the zinba copula distribution |
fitzinba | Fit parameters of a zero inflated negative binomial distribution |
histoneHMM | Analysis of histone modification data using a HMM |
hmm.posterior | HMM posterior |
hmm.viterbi | Viterbi algorithm |
logLikelihood-method | Class 'Distribution' |
LogNormal-class | Class 'Distribution' |
pzinba | Zero inflated negative binomial distribution |
pzinba.copula | Density, CDF and random number generation from a bivariate zinba copula |
run.bivariate.hmm | Bivariate HMM analysis |
run.univariate.hmm | Univariate HMM analysis |
rzinba | Zero inflated negative binomial distribution |
rzinba.copula | Density, CDF and random number generation from a bivariate zinba copula |
Zinba-class | Class 'Distribution' |
zinba.hmm.posterior | Compute state posterior probabilities for a HMM with zinba emission distributions. |
zinbacopula.hmm.posterior | State posterior probabilities for a HMM with zinba copula emission probabilities |