cummeRbund-package	cummeRbund-package
addFeatures	addFeatures
addFeatures,CuffData-method	addFeatures
addFeatures,CuffSet-method	addFeatures
annotation	CuffFeatureSet-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
createDB	createDB
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
csHeatmap	csHeatmap
csHeatmap,CuffFeatureSet-method	csHeatmap
csScatter	csScatter
csScatter,CuffData-method	csScatter
csScatter,CuffFeatureSet-method	csScatter
csSpecificity	csSpecificity
csSpecificity,CuffData-method	csSpecificity
csSpecificity,CuffFeatureSet-method	csSpecificity
csVolcano	csVolcano
csVolcano,CuffData-method	csVolcano
csVolcano,CuffFeatureSet-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
diffData	diffData
diffData,CuffData-method	diffData
diffData,CuffFeature-method	CuffFeature-class
diffData,CuffFeatureSet-method	CuffFeatureSet-class
dim,CuffData-method	CuffData-class
dim,CuffDist-method	CuffDist-class
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	featureNames
featureNames,CuffData-method	featureNames
featureNames,CuffFeatureSet-method	CuffFeatureSet-class
features	features
features,CuffData-method	features
features,CuffFeatureSet-method	CuffFeatureSet-class
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	CuffFeatureSet-class
genes	CuffSet-class
genes,CuffGene-method	CuffGene-class
genes,CuffGeneSet-method	CuffGeneSet-class
genes,CuffSet-method	CuffSet-class
getFeatures,CuffData-method	CuffData-class
getGene	getGene
getGene,CuffSet-method	getGene
getGenes	getGenes
getGenes,CuffSet-method	getGenes
getLevels	getLevels
getLevels,CuffData-method	getLevels
getLevels,CuffSet-method	getLevels
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
makeprobs	makeprobs
makeprobsvec	makeprobsvec
MAplot	MAplot
MAplot,CuffData-method	MAplot
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
sampleGeneSet	sampleGeneSet
sampleIDs	sampleIDs
samples	samples
samples,CuffData-method	samples
samples,CuffDist-method	CuffDist-class
samples,CuffFeatureSet-method	CuffFeatureSet-class
samples,CuffSet-method	samples
shannon.entropy	shannon.entropy
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
[,CuffSet-method	CuffSet-class
