Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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Documentation for package ‘cummeRbund’ version 1.2.0

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A C D E F G I J L M P R S T misc

cummeRbund-package cummeRbund: The finishing touch on your Tuxedo workflow. Analysis, manipulation, and visualization of Cufflinks HTS data. ~~ package title ~~

-- A --

addFeatures addFeatures
addFeatures-method addFeatures
annotation Class "CuffFeatureSet"
annotation-method Class "CuffFeature"
annotation-method Class "CuffFeatureSet"

-- C --

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
csClusterPlot csClusterPlot
csDendro csDendro
csDendro-method csDendro
csDensity Density plot of CuffData
csDensity-method Density plot of CuffData
csHeatmap csHeatmap
csHeatmap-method csHeatmap
csScatter Scatter Plot
csScatter-method Scatter Plot
csSpecificity csSpecificity
csSpecificity-method csSpecificity
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 ~~

-- D --

diffData Differential comparison data
diffData-method Class "CuffFeature"
diffData-method Class "CuffFeatureSet"
diffData-method Differential comparison data
dim-method Class "CuffData"
dim-method Class "CuffDist"
distValues distValues
distValues-method distValues

-- E --

expressionBarplot Barplot
expressionBarplot-method Barplot
expressionPlot Expression Plot
expressionPlot-method Expression Plot

-- F --

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

-- G --

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
getSig getSig
getSig-method getSig
getSigTable getSigTable
getSigTable-method getSigTable

-- I --

isoforms Class "CuffSet"
isoforms-method Class "CuffGene"
isoforms-method Class "CuffGeneSet"
isoforms-method Class "CuffSet"

-- J --

JSdist Jensen-Shannon distance on columns
JSdistFromP Jensen-Shannon distance on rows from a pre-defined vector of probabilities
JSdistVec JSdistVec

-- L --

length-method Class "CuffFeature"
length-method Class "CuffFeatureSet"

-- M --

makeprobs Transform a matrix into probabilities by columns
makeprobsvec makeprobsvec
MAplot MAplot
MAplot-method MAplot

-- P --

PINK1 PINK1
promoters Class "CuffSet"
promoters-method Class "CuffGene"
promoters-method Class "CuffGeneSet"
promoters-method Class "CuffSet"

-- R --

readCufflinks readCufflinks
relCDS Class "CuffSet"
relCDS-method Class "CuffGene"
relCDS-method Class "CuffGeneSet"
relCDS-method Class "CuffSet"

-- S --

sampleGeneSet sampleGeneSet
sampleIDs sampleIDs
samples Get sample list from CuffData object
samples-method Class "CuffDist"
samples-method Class "CuffFeatureSet"
samples-method Get sample list from CuffData object
shannon.entropy Shannon entropy
splicing Class "CuffSet"
splicing-method Class "CuffGene"
splicing-method Class "CuffGeneSet"
splicing-method Class "CuffSet"

-- T --

TSS Class "CuffSet"
TSS-method Class "CuffGene"
TSS-method Class "CuffGeneSet"
TSS-method Class "CuffSet"

-- misc --

[-method Class "CuffSet"