cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, exploration, manipulation, and visualization of Cufflinks HTS data.


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Documentation for package ‘cummeRbund’ version 1.0.0

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