alongChromTicks	Ringo-internal
arrayImage	arrayImage
arrayName	probeAnnoClass
arrayName,probeAnno-method	probeAnnoClass
arrayName<-	probeAnnoClass
arrayName<-,probeAnno,character-method	probeAnnoClass
as.data.frame.cherList	Ringo-internal
asExpressionSet	asExprSet
asExprSet	asExprSet
autocor	autocorr
autocorr	autocorr
autocorrelation	autocorr
cbind2,ExpressionSet,ExpressionSet-method	Ringo-internal
cellType	cherClass
cellType,cher-method	cherClass
cellType<-	cherClass
cellType<-,cher,character-method	cherClass
Cher	cherClass
cher	cherClass
cher-class	cherClass
cherByThreshold	cherByThreshold
cherList	cherClass
cherList-class	cherClass
cherPlot	plot_cher
chersToBED	cherClass
chipAlongChrom	chipAlongChrom
chipAlongChrom1	chipAlongChromOld
chipAlongChromOld	chipAlongChromOld
chromosomeNames	probeAnnoClass
chromosomeNames,probeAnno-method	probeAnnoClass
clusters	Ringo-internal
coerce,environment,probeAnno-method	probeAnnoClass
compute.gc	compute_gc
computeRunningMedians	computeRunningMedians
computeSlidingT	compute_sliding_t
corPlot	corrPlot
corrPlot	corrPlot
createProbeAnno	posToProbeAnnoEnvironment
exportCCData	Ringo-internal
exportCherList	exportCherList
extractProbeAnno	extractProbeAnno
featureColors	Ringo-internal
features2Probes	features2Probes
findChersOnSmoothed	findChersOnSmoothed
ftr2xys	ftr2xys
gccontent	compute_gc
genome	probeAnnoClass
genome,probeAnno-method	probeAnnoClass
genome<-	probeAnnoClass
genome<-,probeAnno,character-method	probeAnnoClass
get,character,missing,probeAnno-method	probeAnnoClass
getFeats	getFeats
getFeatures	getFeats
image,RGList-method	arrayImage
image.RGList	arrayImage
initialize,cher-method	cherClass
initialize,probeAnno-method	probeAnnoClass
ls,probeAnno,missing,missing,missing,missing-method	probeAnnoClass
merge.RGList	Ringo-internal
newCher	newCER
newVP	Ringo-internal
nimblegenScale	nimblegenNorm
nonzero	nonzero
nonzero,dgCMatrix-method	nonzero
nonzero,matrix-method	nonzero
nonzero,matrix.csr-method	nonzero
nonzero-methods	nonzero
normalizeBetweenArraysVSN	Ringo-internal
nullUpperBound	upperBoundNull
oneChannelVSN	Ringo-internal
pair2xys	Ringo-internal
panel.cor	Ringo-internal
panel.scatter	Ringo-internal
plot,cher,ExpressionSet-method	plot_cher
plot,cher,missing-method	plot_cher
plot,ExpressionSet,probeAnno-method	chipAlongChrom
plot,qop,ANY-method	qopS4
plot,qop-method	qopS4
plot.autocor.result	plotAutocorr
plot.cher	plot_cher
plotAlongChromLegend	Ringo-internal
plotAutocor	plotAutocorr
plotBinaryMatrix	plotBM
plotBM	plotBM
plotCher	plot_cher
plotOneChIPSample	Ringo-internal
posToProbeAnno	posToProbeAnnoEnvironment
posToProbeAnnoEnvironment	posToProbeAnnoEnvironment
preprocess	preprocess
probeAnno	probeAnnoClass
probeAnno-class	probeAnnoClass
probeAnnoFromRGList	extractProbeAnno
probes	cherClass
probes,cher-method	cherClass
probes,cherList-method	cherClass
qop-class	qopS4
quantilesOverPositions	quantilesOverPositions
readNgIntensitiesTxt	Ringo-internal
readNimblegen	readNimblegen
readNimblegenHeader	Ringo-internal
region.overlap	regionoverlap
regionOverlap	regionoverlap
relateChers	relateCERs
relateChers2	Ringo-internal
show,cher-method	cherClass
show,probeAnno-method	probeAnnoClass
show,qop-method	qopS4
sigGOTable	sigGOTable
sliding.meansd	sliding_meansd
sliding.quantile	sliding_quantile
slidingquantile	sliding_quantile
splitAndSimplify	Ringo-internal
takeMeanOverGroups	Ringo-internal
twoGaussiansNull	twoGaussiansNull
update,cher-method	cherClass
upperBoundNull	upperBoundNull
validateProbeAnno	validProbeAnno
validProbeAnno	validProbeAnno
[,probeAnno,ANY,ANY,ANY-method	probeAnnoClass
[,probeAnno-method	probeAnnoClass
[<-,probeAnno,ANY,ANY,ANY-method	probeAnnoClass
[<-,probeAnno-method	probeAnnoClass
