API for chromstaR
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
| Global functions | |
|---|---|
| .onAttach | Source code |
| Chromstar | Man page Source code |
| assignGroups | Source code |
| bin2dec | Man page Source code |
| binReads | Man page Source code |
| binned.data | Man page |
| binning | Man page |
| calculate.transition.probs | Source code |
| calculatePeakScores | Source code |
| calculatePeakScores.univariate | Source code |
| callPeaksMultivariate | Man page Source code |
| callPeaksReplicates | Man page Source code |
| callPeaksUnivariate | Man page Source code |
| callPeaksUnivariateAllChr | Man page Source code |
| changeFDR | Man page Source code |
| changeMaxPostCutoff | Man page Source code |
| changeMaxPostCutoff.multivariate | Source code |
| changeMaxPostCutoff.univariate | Source code |
| changePostCutoff | Man page Source code |
| changePostCutoff.multivariate | Source code |
| changePostCutoff.univariate | Source code |
| check.exclusive.table | Source code |
| check.experiment.table | Source code |
| check.integer | Source code |
| check.logical | Source code |
| check.multivariate.model | Source code |
| check.multivariate.modellist | Source code |
| check.nonnegative.integer | Source code |
| check.nonnegative.integer.vector | Source code |
| check.nonnegative.vector | Source code |
| check.positive | Source code |
| check.positive.integer | Source code |
| check.positive.integer.vector | Source code |
| check.positive.vector | Source code |
| check.univariate.model | Source code |
| check.univariate.modellist | Source code |
| chromstaR | Man page |
| chromstaR-objects | Man page |
| chromstaR-package | Man page |
| collapseBins | Man page Source code |
| combinatorialStates | Man page Source code |
| combineMultivariates | Man page Source code |
| combinedHMM | Man page |
| combinedMultiHMM | Man page |
| conversion | Man page |
| dec2bin | Man page Source code |
| differentialScoreMax | Man page Source code |
| differentialScoreSum | Man page Source code |
| differentialScores | Source code |
| dnbinom.mean | Source code |
| dnbinom.prob | Source code |
| dnbinom.size | Source code |
| dnbinom.variance | Source code |
| dzinbinom | Man page Source code |
| enrichmentAtAnnotation | Man page Source code |
| enrichment_analysis | Man page |
| experiment.table | Man page |
| exportBinnedData | Source code |
| exportCombinations | Man page Source code |
| exportCombinedMultivariate | Source code |
| exportCombinedMultivariateCombinations | Source code |
| exportCombinedMultivariateCounts | Source code |
| exportCombinedMultivariatePeaks | Source code |
| exportCounts | Man page Source code |
| exportFiles | Man page |
| exportGRangesAsBedFile | Man page Source code |
| exportMultivariate | Source code |
| exportMultivariateCombinations | Source code |
| exportMultivariateCounts | Source code |
| exportMultivariatePeaks | Source code |
| exportPeaks | Man page Source code |
| exportUnivariateCounts | Source code |
| exportUnivariatePeaks | Source code |
| exportUnivariates | Source code |
| fixedWidthBins | Man page Source code |
| genes_rn4 | Man page |
| genomicFrequencies | Man page Source code |
| getCombinations | Man page Source code |
| getDistinctColors | Man page Source code |
| getMaxPostInPeaks | Source code |
| getMaxPostInPeaks.univariate | Source code |
| getStateColors | Man page Source code |
| get_rightxlim | Source code |
| heatmapCombinations | Man page Source code |
| heatmapCountCorrelation | Man page Source code |
| heatmapTransitionProbs | Man page Source code |
| insertchr | Source code |
| loadHmmsFromFiles | Man page Source code |
| mergeChroms | Man page Source code |
| messageU | Source code |
| model.combined | Man page |
| model.multivariate | Man page |
| model.univariate | Man page |
| multi.hmm | Man page |
| multiHMM | Man page |
| multivariateSegmentation | Man page Source code |
| plotBoxplot | Source code |
| plotEnrichCountHeatmap | Man page Source code |
| plotEnrichment | Man page Source code |
| plotExpression | Man page Source code |
| plotFoldEnrichHeatmap | Man page Source code |
| plotGenomeBrowser | Man page Source code |
| plotHistogram | Man page Source code |
| plotHistograms | Man page Source code |
| plotNormalTransformation | Source code |
| plotting | Man page |
| prepareMultivariate | Source code |
| print.combinedMultiHMM | Man page Source code |
| print.multiHMM | Man page Source code |
| print.uniHMM | Man page Source code |
| pzinbinom | Man page Source code |
| qzinbinom | Man page Source code |
| readBamFileAsGRanges | Man page Source code |
| readBedFileAsGRanges | Man page Source code |
| readConfig | Man page Source code |
| readCustomBedFile | Man page Source code |
| removeCondition | Man page Source code |
| rpkm.matrix | Source code |
| rpkm.vector | Source code |
| runMultivariate | Source code |
| rzinbinom | Man page Source code |
| scanBinsizes | Man page Source code |
| scores | Man page |
| simulateMultivariate | Man page Source code |
| simulateReadsFromCounts | Man page Source code |
| simulateUnivariate | Man page Source code |
| startTimedMessage | Source code |
| state.brewer | Man page Source code |
| stateBrewer | Man page Source code |
| stateorderByTransition | Source code |
| stateswap | Source code |
| stopTimedMessage | Source code |
| subsample | Man page Source code |
| transProbs | Source code |
| transitionFrequencies | Man page Source code |
| uni.hmm | Man page |
| uniHMM | Man page |
| unis2pseudomulti | Man page Source code |
| variableWidthBins | Man page Source code |
| writeConfig | Man page Source code |
| zinbinom | Man page |
