AneuFinder-package	AneuFinder-package
aneuBiHMM	aneuBiHMM
AneuFinder	AneuFinder-package
Aneufinder	Aneufinder
aneuHMM	aneuHMM
bam2GRanges	bam2GRanges
bed2GRanges	bed2GRanges
biDNAcopy.findCNVs	biDNAcopy.findCNVs
binned.data	binned.data
binning	binning
binReads	binReads
bivariate.findCNVs	bivariate.findCNVs
blacklist	blacklist
clusterByQuality	clusterByQuality
collapseBins	collapseBins
colors	colors
compareMethods	compareMethods
compareModels	compareModels
consensusSegments	consensusSegments
correctGC	correctGC
correctMappability	correctMappability
deltaWCalculator	deltaWCalculator
DNAcopy.findCNVs	DNAcopy.findCNVs
dzinbinom	zinbinom
estimateComplexity	estimateComplexity
export	export
exportCNVs	export
exportGRanges	export
exportReadCounts	export
filterSegments	filterSegments
findBreakpoints	findBreakpoints
findCNVs	findCNVs
findCNVs.strandseq	findCNVs.strandseq
fixedWidthBins	fixedWidthBins
getDistinctColors	getDistinctColors
getQC	getQC
getSCEcoordinates	getSCEcoordinates
getSegments	getSegments
heatmapAneuploidies	heatmapAneuploidies
heatmapGenomewide	heatmapGenomewide
heatmapGenomewideClusters	heatmapGenomewideClusters
hotspotter	hotspotter
importBed	importBed
initializeStates	initializeStates
karyotypeMeasures	karyotypeMeasures
loadFromFiles	loadFromFiles
mergeStrandseqFiles	mergeStrandseqFiles
plot.aneuBiHMM	plot.aneuBiHMM
plot.aneuHMM	plot.aneuHMM
plot.character	plot.character
plot.GRanges	plot.GRanges
plotHeterogeneity	plotHeterogeneity
plotHistogram	plotHistogram
plotKaryogram	plotKaryogram
plotProfile	plotProfile
plot_pca	plot_pca
print.aneuBiHMM	print.aneuBiHMM
print.aneuHMM	print.aneuHMM
pzinbinom	zinbinom
qc.bhattacharyya	qualityControl
qc.entropy	qualityControl
qc.sos	qualityControl
qc.spikiness	qualityControl
qualityControl	qualityControl
qzinbinom	zinbinom
readConfig	readConfig
rzinbinom	zinbinom
simulateReads	simulateReads
stateColors	colors
strandColors	colors
subsetByCNVprofile	subsetByCNVprofile
transCoord	transCoord
univariate.findCNVs	univariate.findCNVs
variableWidthBins	variableWidthBins
writeConfig	writeConfig
zinbinom	zinbinom
