API for plbaldoni/epigraHMM
Epigenomic R-based analysis with hidden Markov models
| Global functions | |
|---|---|
| addOffsets | Man page Source code |
| aggregate | Source code |
| aggregateCounts | Source code |
| callPatterns | Man page Source code |
| callPeaks | Man page Source code |
| checkConvergence | Source code |
| checkInputBam | Source code |
| checkInputMatrix | Source code |
| checkPath | Source code |
| checkPlot | Source code |
| checkProbabilities | Source code |
| cleanCounts | Man page Source code |
| computeBIC | Source code |
| computeQFunction | Source code |
| computeViterbiSequence | Source code |
| consensusHMM | Source code |
| consensusRejectionControlled | Source code |
| controlEM | Man page Source code |
| controlList | Source code |
| derivMixNB | Source code |
| derivMixZINB | Source code |
| derivNB | Source code |
| derivZINB | Source code |
| determineMixtures | Source code |
| differentialHMM | Source code |
| differentialRejectionControlled | Source code |
| dzinb | Source code |
| emConsensus | Source code |
| emInitialization | Source code |
| enumeratePatterns | Source code |
| epigraHMM | Man page Source code |
| epigraHMMDataSetFromBam | Man page Source code |
| epigraHMMDataSetFromMatrix | Man page Source code |
| estimateCoefficients | Source code |
| estimateMixtureProb | Source code |
| estimateTransitionProb | Man page Source code |
| expStep | Man page Source code |
| fdrControl | Source code |
| generateMixtureIntercepts | Source code |
| getError | Source code |
| getFragLen | Source code |
| getGap | Source code |
| getGenome | Source code |
| getList | Source code |
| getMarginalProbability | Source code |
| getPatterns | Source code |
| glmMixNB | Source code |
| glmMixZINB | Source code |
| glmNB | Source code |
| glmZINB | Source code |
| helas3 | Man page |
| info | Man page Source code |
| initializer | Man page Source code |
| initializerHMM | Source code |
| innerEMDifferential | Source code |
| innerExpStep | Source code |
| innerMaxStepProb | Source code |
| invertDispersion | Source code |
| loglikConsensusHMM | Source code |
| loglikDifferential | Source code |
| loglikDifferentialHMM | Source code |
| maxStepProb | Man page Source code |
| meltCounts | Source code |
| normalizeCounts | Man page Source code |
| optimDifferential | Source code |
| optimNB | Source code |
| outerEMDifferential | Source code |
| plotCounts | Man page Source code |
| plotPatterns | Man page Source code |
| posteriorProbPlot | Source code |
| prunePatterns | Source code |
| rbinomVectorized | Source code |
| readCountPlot | Source code |
| reweight | Source code |
| saveOutputFiles | Source code |
| segmentGenome | Man page Source code |
| simulateMarkovChain | Man page Source code |
| sortObject | Source code |
| verbose | Source code |
| verbosePrunning | Source code |
| writeBed | Source code |
| writeBedGraph | Source code |
| writeWig | Source code |
