cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, manipulation, and visualization of Cufflinks HTS data.
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csDendro
PINK1
Class "CuffSet"
Class "CuffFeatureSet"
Class "CuffDist"
Differential comparison data
Class "CuffData"
Shannon entropy
csClusterPlot
csDistHeat
Get sample list from CuffData object
sampleGeneSet
getLevels
getSig
Volcano Plot
Get replicate sample list from CuffData object
getGenes
findGene
csHeatmap
Quality Control visualizations
Class "CuffFeature"
Scatter Plot
fpkmMatrix
Retrieve FPKM values
Mean count vs dispersion plot
findSimilar
Barplot
getGene
Jensen-Shannon distance on rows from a pre-defined vector of probabilities
distValues
Class "CuffGene"
Dimensionality reduction utilities
csCluster
Transform a matrix into probabilities by columns
countMatrix
getRepLevels
Retrieve run parameters and information from a CuffSet object
MAplot
Retrieve count values (raw and normalized)
addFeatures
Expression Plot
Feature names
getGene
Retrieve FPKM values
Class "CuffGeneSet"
Jensen-Shannon distance on columns
Density plot of CuffData
Methods for Exploratory Analysis in cummeRbund
getFeatures
Features
readCufflinks
JSdistVec
sigMatrix
csBoxplot
csSpecificity
getSigTable
makeprobsvec
sampleIDs