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
JSdistFromP             Jensen-Shannon distance on rows from a
                        pre-defined vector of probabilities
JSdistVec               JSdistVec
MAplot                  MAplot
PINK1                   PINK1
addFeatures             addFeatures
createDB                createDB
csBoxplot               csBoxplot
csCluster               csCluster
csClusterPlot           csClusterPlot
csDendro                csDendro
csDensity               Density plot of CuffData
csHeatmap               csHeatmap
csScatter               Scatter Plot
csSpecificity           csSpecificity
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
getSig                  getSig
getSigTable             getSigTable
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
