Man pages for Bioconductor-mirror/cummeRbund
Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

addFeaturesaddFeatures
countRetrieve count values (raw and normalized)
countMatrixcountMatrix
csBoxplotcsBoxplot
csClustercsCluster
csClusterPlotcsClusterPlot
csDendrocsDendro
csDensityDensity plot of CuffData
csDistHeatcsDistHeat
csHeatmapcsHeatmap
csScatterScatter Plot
csSpecificitycsSpecificity
csVolcanoVolcano Plot
CuffData-classClass "CuffData"
CuffDist-classClass "CuffDist"
CuffFeature-classClass "CuffFeature"
CuffFeatureSet-classClass "CuffFeatureSet"
CuffGene-classClass "CuffGene"
CuffGeneSet-classClass "CuffGeneSet"
CuffSet-classClass "CuffSet"
cummeRbund-packagecummeRbund: The finishing touch on your Tuxedo workflow....
diffDataDifferential comparison data
dimensionalityDimensionality reduction utilities
dispersionPlotMean count vs dispersion plot
distValuesdistValues
exploratoryMethods for Exploratory Analysis in cummeRbund
expressionBarplotBarplot
expressionPlotExpression Plot
featureNamesFeature names
featuresFeatures
findGenefindGene
findSimilarfindSimilar
fpkmRetrieve FPKM values
fpkmMatrixfpkmMatrix
getFeaturesgetFeatures
getGenegetGene
getGeneIdgetGene
getGenesgetGenes
getLevelsgetLevels
getRepLevelsgetRepLevels
getSiggetSig
getSigTablegetSigTable
JSdistJensen-Shannon distance on columns
JSdistFromPJensen-Shannon distance on rows from a pre-defined vector of...
JSdistVecJSdistVec
makeprobsTransform a matrix into probabilities by columns
makeprobsvecmakeprobsvec
MAplotMAplot
PINK1PINK1
QCplotsQuality Control visualizations
readCufflinksreadCufflinks
repFpkmRetrieve FPKM values
replicatesGet replicate sample list from CuffData object
runInfoRetrieve run parameters and information from a CuffSet object
sampleGeneSetsampleGeneSet
sampleIDssampleIDs
samplesGet sample list from CuffData object
shannon.entropyShannon entropy
sigMatrixsigMatrix
Bioconductor-mirror/cummeRbund documentation built on Aug. 12, 2017, 5:14 p.m.