AneuFinder-package	AneuFinder-package
aneuBiHMM	aneuBiHMM
AneuFinder	AneuFinder-package
Aneufinder	Aneufinder
aneuHMM	aneuHMM
annotateBreakpoints	annotateBreakpoints
bam2GRanges	bam2GRanges
bed2GRanges	bed2GRanges
bi.edivisive.findCNVs	bi.edivisive.findCNVs
biDNAcopy.findCNVs	biDNAcopy.findCNVs
biHMM.findCNVs	biHMM.findCNVs
binned.data	binned.data
binning	binning
binReads	binReads
blacklist	blacklist
breakpointColors	colors
clusterByQuality	clusterByQuality
clusterHMMs	clusterHMMs
collapseBins	collapseBins
colors	colors
compareMethods	compareMethods
compareModels	compareModels
consensusSegments	consensusSegments
correctGC	correctGC
DNAcopy.findCNVs	DNAcopy.findCNVs
dzinbinom	zinbinom
edivisive.findCNVs	edivisive.findCNVs
estimateComplexity	estimateComplexity
export	export
exportCNVs	export
exportGRanges	export
exportReadCounts	export
filterSegments	filterSegments
findCNVs	findCNVs
findCNVs.strandseq	findCNVs.strandseq
findHotspots	findHotspots
fixedWidthBins	fixedWidthBins
getBreakpoints	getBreakpoints
getDistinctColors	getDistinctColors
getQC	getQC
getSCEcoordinates	getSCEcoordinates
heatmapAneuploidies	heatmapAneuploidies
heatmapGenomewide	heatmapGenomewide
heatmapGenomewideClusters	heatmapGenomewideClusters
HMM.findCNVs	HMM.findCNVs
hotspotter	hotspotter
hotspotter.variable	hotspotter.variable
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
plot.GRangesList	plot.GRangesList
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
refineBreakpoints	refineBreakpoints
rzinbinom	zinbinom
simulateReads	simulateReads
stateColors	colors
strandColors	colors
subsetByCNVprofile	subsetByCNVprofile
transCoord	transCoord
variableWidthBins	variableWidthBins
writeConfig	writeConfig
zinbinom	zinbinom
