cummeRbund-package	cummeRbund-package
addFeatures	addFeatures
addFeatures,CuffData-method	addFeatures
addFeatures,CuffSet-method	addFeatures
annotation	CuffFeatureSet-class
annotation,CuffData-method	CuffData-class
annotation,CuffFeature-method	CuffFeature-class
annotation,CuffFeatureSet-method	CuffFeatureSet-class
CDS	CuffSet-class
CDS,CuffGene-method	CuffGene-class
CDS,CuffGeneSet-method	CuffGeneSet-class
CDS,CuffSet-method	CuffSet-class
conditions	CuffSet-class
conditions,CuffSet-method	CuffSet-class
count	count
count,CuffData-method	count
count,CuffFeature-method	count
count,CuffFeatureSet-method	count
count-methods	count
countMatrix	countMatrix
countMatrix,CuffData-method	countMatrix
countMatrix,CuffFeatureSet-method	countMatrix
csBoxplot	csBoxplot
csBoxplot,CuffData-method	csBoxplot
csCluster	csCluster
csCluster,CuffFeatureSet-method	csCluster
csClusterPlot	csClusterPlot
csDendro	csDendro
csDendro,CuffData-method	csDendro
csDendro,CuffFeatureSet-method	csDendro
csDensity	csDensity
csDensity,CuffData-method	csDensity
csDensity,CuffFeatureSet-method	csDensity
csDistHeat	csDistHeat
csDistHeat,CuffData-method	csDistHeat
csDistHeat,CuffFeatureSet-method	csDistHeat
csFoldChangeHeatmap	csHeatmap
csFoldChangeHeatmap,CuffFeatureSet-method	csHeatmap
csHeatmap	csHeatmap
csHeatmap,CuffFeatureSet-method	csHeatmap
csNMF	exploratory
csNMF,CuffData-method	exploratory
csNMF,CuffFeatureSet-method	exploratory
csPie	CuffGene-class
csPie,CuffGene-method	CuffGene-class
csScatter	csScatter
csScatter,CuffData-method	csScatter
csScatter,CuffFeatureSet-method	csScatter
csScatterMatrix	csScatter
csScatterMatrix,CuffData-method	csScatter
csSpecificity	csSpecificity
csSpecificity,CuffData-method	csSpecificity
csSpecificity,CuffFeatureSet-method	csSpecificity
csVolcano	csVolcano
csVolcano,CuffData-method	csVolcano
csVolcano,CuffFeatureSet-method	csVolcano
csVolcanoMatrix	csVolcano
csVolcanoMatrix,CuffData-method	csVolcano
CuffData-class	CuffData-class
CuffDist-class	CuffDist-class
CuffFeature-class	CuffFeature-class
CuffFeatureSet-class	CuffFeatureSet-class
CuffGene-class	CuffGene-class
CuffGeneSet-class	CuffGeneSet-class
CuffSet-class	CuffSet-class
cummeRbund	cummeRbund-package
DB	CuffSet-class
DB,CuffData-method	CuffData-class
DB,CuffDist-method	CuffDist-class
DB,CuffSet-method	CuffSet-class
diffData	diffData
diffData,CuffData-method	diffData
diffData,CuffFeature-method	CuffFeature-class
diffData,CuffFeatureSet-method	CuffFeatureSet-class
diffTable	diffData
diffTable,CuffData-method	diffData
diffTable,CuffFeatureSet-method	diffData
dim,CuffData-method	CuffData-class
dim,CuffDist-method	CuffDist-class
dispersionPlot	dispersionPlot
dispersionPlot,CuffData-method	dispersionPlot
dispersionPlot,CuffSet-method	dispersionPlot
distValues	distValues
distValues,CuffDist-method	distValues
expressionBarplot	expressionBarplot
expressionBarplot,CuffFeature-method	expressionBarplot
expressionBarplot,CuffFeatureSet-method	expressionBarplot
expressionPlot	expressionPlot
expressionPlot,CuffFeature-method	expressionPlot
expressionPlot,CuffFeatureSet-method	expressionPlot
featureNames,CuffData-method	featureNames
featureNames,CuffFeatureSet-method	CuffFeatureSet-class
features	features
features,CuffFeatureSet-method	CuffFeatureSet-class
features,CuffGene-method	features
findGene	findGene
findGene,CuffSet-method	findGene
findSimilar	findSimilar
findSimilar,CuffSet-method	findSimilar
fpkm	fpkm
fpkm,CuffData-method	fpkm
fpkm,CuffFeature-method	fpkm
fpkm,CuffFeatureSet-method	fpkm
fpkm-methods	fpkm
fpkmMatrix	fpkmMatrix
fpkmMatrix,CuffData-method	fpkmMatrix
fpkmMatrix,CuffFeature-method	CuffFeature-class
fpkmMatrix,CuffFeatureSet-method	fpkmMatrix
fpkmSCVPlot	QCplots
fpkmSCVPlot,CuffData-method	QCplots
genePlot	CuffGene-class
genePlot,CuffGene-method	CuffGene-class
genes	CuffSet-class
genes,CuffGene-method	CuffGene-class
genes,CuffGeneSet-method	CuffGeneSet-class
genes,CuffSet-method	CuffSet-class
getFeatures	getFeatures
getFeatures,CuffData-method	CuffData-class
getFeatures,CuffSet-method	getFeatures
getGene	getGene
getGene,CuffSet-method	getGene
getGeneId	getGeneId
getGeneId,CuffSet-method	getGeneId
getGenes	getGenes
getGenes,CuffSet-method	getGenes
getLevels	getLevels
getLevels,CuffData-method	getLevels
getLevels,CuffSet-method	getLevels
getRepLevels	getRepLevels
getRepLevels,CuffData-method	getRepLevels
getRepLevels,CuffSet-method	getRepLevels
getSig	getSig
getSig,CuffSet-method	getSig
getSigTable	getSigTable
getSigTable,CuffSet-method	getSigTable
isoforms	CuffSet-class
isoforms,CuffGene-method	CuffGene-class
isoforms,CuffGeneSet-method	CuffGeneSet-class
isoforms,CuffSet-method	CuffSet-class
JSdist	JSdist
JSdistFromP	JSdistFromP
JSdistVec	JSdistVec
length,CuffFeature-method	CuffFeature-class
length,CuffFeatureSet-method	CuffFeatureSet-class
length,CuffGene-method	CuffGene-class
makeGeneRegionTrack	CuffGene-class
makeGeneRegionTrack,CuffGene-method	CuffGene-class
makeprobs	makeprobs
makeprobsvec	makeprobsvec
makeRnk	CuffData-class
makeRnk,CuffData-method	CuffData-class
MAplot	MAplot
MAplot,CuffData-method	MAplot
MDSplot	dimensionality
MDSplot,CuffData-method	dimensionality
MDSplot,CuffFeatureSet-method	dimensionality
PCAplot	dimensionality
PCAplot,CuffData-method	dimensionality
PCAplot,CuffFeatureSet-method	dimensionality
PINK1	PINK1
promoters	CuffSet-class
promoters,CuffGene-method	CuffGene-class
promoters,CuffGeneSet-method	CuffGeneSet-class
promoters,CuffSet-method	CuffSet-class
readCufflinks	readCufflinks
relCDS	CuffSet-class
relCDS,CuffGene-method	CuffGene-class
relCDS,CuffGeneSet-method	CuffGeneSet-class
relCDS,CuffSet-method	CuffSet-class
repCountMatrix	countMatrix
repCountMatrix,CuffData-method	countMatrix
repCountMatrix,CuffFeatureSet-method	countMatrix
repFpkm	repFpkm
repFpkm,CuffData-method	repFpkm
repFpkm,CuffFeature-method	repFpkm
repFpkm,CuffFeatureSet-method	repFpkm
repFpkm-methods	repFpkm
repFpkmMatrix	fpkmMatrix
repFpkmMatrix,CuffData-method	fpkmMatrix
repFpkmMatrix,CuffFeature-method	fpkmMatrix
repFpkmMatrix,CuffFeatureSet-method	fpkmMatrix
replicates	replicates
replicates,CuffData-method	replicates
replicates,CuffFeature-method	replicates
replicates,CuffFeatureSet-method	replicates
replicates,CuffSet-method	replicates
runInfo	runInfo
runInfo,CuffSet-method	runInfo
sampleGeneSet	sampleGeneSet
sampleIDs	sampleIDs
samples	samples
samples,CuffData-method	samples
samples,CuffDist-method	CuffDist-class
samples,CuffFeature-method	CuffFeature-class
samples,CuffFeatureSet-method	CuffFeatureSet-class
samples,CuffSet-method	samples
shannon.entropy	shannon.entropy
sigMatrix	sigMatrix
sigMatrix,CuffSet-method	sigMatrix
splicing	CuffSet-class
splicing,CuffGene-method	CuffGene-class
splicing,CuffGeneSet-method	CuffGeneSet-class
splicing,CuffSet-method	CuffSet-class
TSS	CuffSet-class
TSS,CuffGene-method	CuffGene-class
TSS,CuffGeneSet-method	CuffGeneSet-class
TSS,CuffSet-method	CuffSet-class
varModel	CuffSet-class
varModel,CuffSet-method	CuffSet-class
[,CuffSet-method	CuffSet-class
