chromstaR-package	chromstaR-package
bin2dec	conversion
binned.data	binned.data
binning	binReads
binReads	binReads
callPeaksMultivariate	callPeaksMultivariate
callPeaksReplicates	callPeaksReplicates
callPeaksUnivariate	callPeaksUnivariate
callPeaksUnivariateAllChr	callPeaksUnivariateAllChr
changeFDR	changeMaxPostCutoff
changeMaxPostCutoff	changeMaxPostCutoff
changePostCutoff	changePostCutoff
Chromstar	Chromstar
chromstaR	chromstaR-package
chromstaR-objects	chromstaR-objects
collapseBins	collapseBins
combinatorialStates	combinatorialStates
combinedHMM	combinedMultiHMM
combinedMultiHMM	combinedMultiHMM
combineMultivariates	combineMultivariates
conversion	conversion
dec2bin	conversion
differentialScoreMax	scores
differentialScoreSum	scores
dzinbinom	zinbinom
enrichmentAtAnnotation	enrichmentAtAnnotation
enrichment_analysis	enrichment_analysis
experiment.table	experiment.table
exportCombinations	exportFiles
exportCounts	exportFiles
exportFiles	exportFiles
exportGRangesAsBedFile	exportGRangesAsBedFile
exportPeaks	exportFiles
fixedWidthBins	fixedWidthBins
genes_rn4	genes_rn4
genomicFrequencies	genomicFrequencies
getCombinations	getCombinations
getDistinctColors	getDistinctColors
getStateColors	getStateColors
heatmapCombinations	heatmapCombinations
heatmapCountCorrelation	heatmapCountCorrelation
heatmapTransitionProbs	heatmapTransitionProbs
loadHmmsFromFiles	loadHmmsFromFiles
mergeChroms	mergeChroms
model.combined	model.combined
model.multivariate	model.multivariate
model.univariate	model.univariate
multi.hmm	multiHMM
multiHMM	multiHMM
multivariateSegmentation	multivariateSegmentation
plotEnrichCountHeatmap	enrichment_analysis
plotEnrichment	enrichment_analysis
plotExpression	plotExpression
plotFoldEnrichHeatmap	enrichment_analysis
plotGenomeBrowser	plotGenomeBrowser
plotHistogram	plotHistogram
plotHistograms	plotHistograms
plotting	plotting
print.combinedMultiHMM	print.combinedMultiHMM
print.multiHMM	print.multiHMM
print.uniHMM	print.uniHMM
pzinbinom	zinbinom
qzinbinom	zinbinom
readBamFileAsGRanges	readBamFileAsGRanges
readBedFileAsGRanges	readBedFileAsGRanges
readConfig	readConfig
readCustomBedFile	readCustomBedFile
removeCondition	removeCondition
rzinbinom	zinbinom
scanBinsizes	scanBinsizes
scores	scores
simulateMultivariate	simulateMultivariate
simulateReadsFromCounts	simulateReadsFromCounts
simulateUnivariate	simulateUnivariate
state.brewer	state.brewer
stateBrewer	stateBrewer
subsample	subsample
transitionFrequencies	transitionFrequencies
uni.hmm	uniHMM
uniHMM	uniHMM
unis2pseudomulti	unis2pseudomulti
variableWidthBins	variableWidthBins
writeConfig	writeConfig
zinbinom	zinbinom
