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
MDSplot                 Dimensionality reduction utilities
PINK1                   PINK1
addFeatures             addFeatures
count-methods           Retrieve count values (raw and normalized)
countMatrix             countMatrix
csBoxplot               csBoxplot
csCluster               csCluster
csClusterPlot           csClusterPlot
csDendro                csDendro
csDensity               Density plot of CuffData
csDistHeat              csDistHeat
csHeatmap               csHeatmap
csNMF                   Methods for Exploratory Analysis in cummeRbund
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
dispersionPlot          Mean count vs dispersion plot
distValues              distValues
expressionBarplot       Barplot
expressionPlot          Expression Plot
featureNames,CuffData-method
                        Feature names
features                Features
findGene                findGene
findSimilar             findSimilar
fpkm-methods            Retrieve FPKM values
fpkmMatrix              fpkmMatrix
fpkmSCVPlot             Quality Control visualizations
getFeatures             getFeatures
getGene                 getGene
getGeneId               getGene
getGenes                getGenes
getLevels               getLevels
getRepLevels            getRepLevels
getSig                  getSig
getSigTable             getSigTable
makeprobs               Transform a matrix into probabilities by
                        columns
makeprobsvec            makeprobsvec
readCufflinks           readCufflinks
repFpkm-methods         Retrieve FPKM values
replicates              Get replicate sample list from CuffData object
runInfo                 Retrieve run parameters and information from a
                        CuffSet object
sampleGeneSet           sampleGeneSet
sampleIDs               sampleIDs
samples                 Get sample list from CuffData object
shannon.entropy         Shannon entropy
sigMatrix               sigMatrix
