CuffData-class          Class "CuffData"
CuffDist-class          Class "CuffDist"
CuffFeature-class       Class "CuffFeature"
CuffFeatureSet-class    Class "CuffFeatureSet"
CuffGene-class          Class "CuffGene"
CuffGeneSet-class       Class "CuffGeneSet"
CuffSet-class           Class "CuffSet"
JSdist                  Jensen-Shannon distance on columns
JSdistVec               JSdistVec
PINK1                   PINK1
addFeatures             addFeatures
createDB                createDB
csBoxplot               csBoxplot
csCluster               csCluster
csDensity               Density plot of CuffData
csHeatmap               csHeatmap
csScatter               Scatter Plot
csVolcano               Volcano Plot
cummeRbund-package      cummeRbund: The finishing touch on your Tuxedo
                        workflow. Analysis, manipulation, and
                        visualization of Cufflinks HTS data. ~~ package
                        title ~~
diffData                Differential comparison data
distValues              distValues
expressionBarplot       Barplot
expressionPlot          Expression Plot
featureNames            Feature names
features                Features
findSimilar             findSimilar
fpkm-methods            Retrieve FPKM values
fpkmMatrix              fpkmMatrix
getGene                 getGene
getGenes                getGenes
getLevels               getLevels
makeprobs               Transform a matrix into probabilities by
                        columns
makeprobsvec            makeprobsvec
readCufflinks           readCufflinks
sampleGeneSet           sampleGeneSet
sampleIDs               sampleIDs
samples                 Get sample list from CuffData object
shannon.entropy         Shannon entropy
