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

## Documentation for package ‘cummeRbund’ version 2.12.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A C D E F G I J L M P R S T V 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 "CuffData"
annotation-method | Class "CuffFeature"
annotation-method | Class "CuffFeatureSet"

## -- C --

CDS | Class "CuffSet"
CDS-method | Class "CuffGene"
CDS-method | Class "CuffGeneSet"
CDS-method | Class "CuffSet"
conditions | Class "CuffSet"
conditions-method | Class "CuffSet"
count | Retrieve count values (raw and normalized)
count-method | Retrieve count values (raw and normalized)
count-methods | Retrieve count values (raw and normalized)
countMatrix | countMatrix
countMatrix-method | countMatrix
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
csDistHeat | csDistHeat
csDistHeat-method | csDistHeat
csFoldChangeHeatmap | csHeatmap
csFoldChangeHeatmap-method | csHeatmap
csHeatmap | csHeatmap
csHeatmap-method | csHeatmap
csNMF | Methods for Exploratory Analysis in cummeRbund
csNMF-method | Methods for Exploratory Analysis in cummeRbund
csPie | Class "CuffGene"
csPie-method | Class "CuffGene"
csScatter | Scatter Plot
csScatter-method | Scatter Plot
csScatterMatrix | Scatter Plot
csScatterMatrix-method | Scatter Plot
csSpecificity | csSpecificity
csSpecificity-method | csSpecificity
csVolcano | Volcano Plot
csVolcano-method | Volcano Plot
csVolcanoMatrix | Volcano Plot
csVolcanoMatrix-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 --

DB | Class "CuffSet"
DB-method | Class "CuffData"
DB-method | Class "CuffDist"
DB-method | Class "CuffSet"
diffData | Differential comparison data
diffData-method | Class "CuffFeature"
diffData-method | Class "CuffFeatureSet"
diffData-method | Differential comparison data
diffTable | Differential comparison data
diffTable-method | Differential comparison data
dim-method | Class "CuffData"
dim-method | Class "CuffDist"
dispersionPlot | Mean count vs dispersion plot
dispersionPlot-method | Mean count vs dispersion plot
distValues | distValues
distValues-method | distValues

## -- E --

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

## -- F --

featureNames-method | Class "CuffFeatureSet"
featureNames-method | Feature names
features | Features
features-method | Class "CuffFeatureSet"
features-method | Features
findGene | findGene
findGene-method | findGene
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 | fpkmMatrix
fpkmSCVPlot | Quality Control visualizations
fpkmSCVPlot-method | Quality Control visualizations

## -- G --

genePlot | Class "CuffGene"
genePlot-method | Class "CuffGene"
genes | Class "CuffSet"
genes-method | Class "CuffGene"
genes-method | Class "CuffGeneSet"
genes-method | Class "CuffSet"
getFeatures | getFeatures
getFeatures-method | Class "CuffData"
getFeatures-method | getFeatures
getGene | getGene
getGene-method | getGene
getGeneId | getGene
getGeneId-method | getGene
getGenes | getGenes
getGenes-method | getGenes
getLevels | getLevels
getLevels-method | getLevels
getRepLevels | getRepLevels
getRepLevels-method | getRepLevels
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"
length-method | Class "CuffGene"

## -- M --

makeGeneRegionTrack | Class "CuffGene"
makeGeneRegionTrack-method | Class "CuffGene"
makeprobs | Transform a matrix into probabilities by columns
makeprobsvec | makeprobsvec
makeRnk | Class "CuffData"
makeRnk-method | Class "CuffData"
MAplot | MAplot
MAplot-method | MAplot
MDSplot | Dimensionality reduction utilities
MDSplot-method | Dimensionality reduction utilities

## -- P --

PCAplot | Dimensionality reduction utilities
PCAplot-method | Dimensionality reduction utilities
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"
repCountMatrix | countMatrix
repCountMatrix-method | countMatrix
repFpkm | Retrieve FPKM values
repFpkm-method | Retrieve FPKM values
repFpkm-methods | Retrieve FPKM values
repFpkmMatrix | fpkmMatrix
repFpkmMatrix-method | fpkmMatrix
replicates | Get replicate sample list from CuffData object
replicates-method | Get replicate sample list from CuffData object
runInfo | Retrieve run parameters and information from a CuffSet object
runInfo-method | Retrieve run parameters and information from a CuffSet object

## -- S --

sampleGeneSet | sampleGeneSet
sampleIDs | sampleIDs
samples | Get sample list from CuffData object
samples-method | Class "CuffDist"
samples-method | Class "CuffFeature"
samples-method | Class "CuffFeatureSet"
samples-method | Get sample list from CuffData object
shannon.entropy | Shannon entropy
sigMatrix | sigMatrix
sigMatrix-method | sigMatrix
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"

## -- V --

varModel | Class "CuffSet"
varModel-method | Class "CuffSet"

## -- misc --

[-method | Class "CuffSet"