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

Package index
Search the cummeRbund package
Vignettes
Functions
336
Source code
13
Man pages
59
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cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.
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API

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

Global functions
.CVdensity Source code
.MAplot Source code
.MDSplot Source code
.PCAplot Source code
.QCTable Source code
.addFeatures Source code Source code
.annotation Source code Source code
.as.GRanges Source code
.as.GRangesList Source code
.barplot Source code
.boxplot Source code
.checkReps Source code
.checkSamples Source code Source code
.confidencePlot Source code
.count Source code Source code Source code
.countMatrix Source code Source code
.cuff2db Source code
.dendro Source code
.density Source code
.dfToJSONarray Source code
.diffData Source code Source code Source code
.diffTable Source code Source code
.dispersionPlot Source code Source code
.distheat Source code
.expressionPlot Source code
.featureNames Source code Source code
.findGene Source code
.findSimilar Source code
.fpkm Source code Source code Source code
.fpkmMatrix Source code Source code Source code
.fpkmSCVPlot Source code
.getCountMA Source code
.getFeatures Source code
.getGene Source code
.getGeneId Source code
.getGenes Source code
.getGenome Source code
.getLevels Source code Source code
.getMA Source code
.getRepConditionLevels Source code
.getRepLevels Source code Source code
.getSig Source code
.getSigTable Source code
.ggheat Source code
.hclustToJSON Source code
.heatmap Source code
.ideogram Source code
.loadGTF Source code
.makeGRanges Source code
.makeGeneRegionTrack Source code
.makeRnk Source code
.makeRnkTest Source code
.makeRnkTestStat Source code
.nmf Source code
.pie Source code
.plot Source code
.plot2 Source code
.recordGenome Source code
.repCountMatrix Source code Source code
.repFpkm Source code Source code Source code
.repFpkmMatrix Source code Source code Source code
.replicates Source code Source code Source code Source code
.runInfo Source code
.samples Source code Source code Source code Source code Source code
.scatter Source code
.scatter2 Source code
.scatterMat Source code
.sensitivityPlot Source code
.sigMatrix Source code
.specificity Source code Source code
.statsMatrix Source code
.values Source code
.varModel Source code
.volcano Source code
.volcanoMatrix Source code
CDS Man page
CDS,CuffGene-method Man page
CDS,CuffGeneSet-method Man page
CDS,CuffSet-method Man page
CuffData-class Man page
CuffDist-class Man page
CuffFeature-class Man page
CuffFeatureSet-class Man page
CuffGene-class Man page
CuffGeneSet-class Man page
CuffSet-class Man page
DB Man page
DB,CuffData-method Man page
DB,CuffDist-method Man page
DB,CuffSet-method Man page
JSdist Man page Source code
JSdistFromP Man page Source code
JSdistVec Man page Source code
JSdivVec Source code
MAplot Man page
MAplot,CuffData-method Man page
MDSplot Man page
MDSplot,CuffData-method Man page
MDSplot,CuffFeatureSet-method Man page
PCAplot Man page
PCAplot,CuffData-method Man page
PCAplot,CuffFeatureSet-method Man page
PINK1 Man page
TSS Man page
TSS,CuffGene-method Man page
TSS,CuffGeneSet-method Man page
TSS,CuffSet-method Man page
[,CuffSet-method Man page
addFeatures Man page
addFeatures,CuffData-method Man page
addFeatures,CuffSet-method Man page
annotation Man page
annotation,CuffData-method Man page
annotation,CuffFeature-method Man page
annotation,CuffFeatureSet-method Man page
bulk_insert Source code
conditions Man page
conditions,CuffSet-method Man page
count Man page
count,CuffData-method Man page
count,CuffFeature-method Man page
count,CuffFeatureSet-method Man page
count-methods Man page
countMatrix Man page
countMatrix,CuffData-method Man page
countMatrix,CuffFeatureSet-method Man page
createDB_noIndex Source code
createIndices Source code
csBoxplot Man page
csBoxplot,CuffData-method Man page
csCluster Man page
csCluster,CuffFeatureSet-method Man page
csClusterPlot Man page
csDendro Man page
csDendro,CuffData-method Man page
csDendro,CuffFeatureSet-method Man page
csDensity Man page
csDensity,CuffData-method Man page
csDensity,CuffFeatureSet-method Man page
csDistHeat Man page
csDistHeat,CuffData-method Man page
csDistHeat,CuffFeatureSet-method Man page
csFoldChangeHeatmap Man page
csFoldChangeHeatmap,CuffFeatureSet-method Man page
csHeatmap Man page
csHeatmap,CuffFeatureSet-method Man page
csNMF Man page
csNMF,CuffData-method Man page
csNMF,CuffFeatureSet-method Man page
csPie Man page
csPie,CuffGene-method Man page
csScatter Man page
csScatter,CuffData-method Man page
csScatter,CuffFeatureSet-method Man page
csScatterMatrix Man page
csScatterMatrix,CuffData-method Man page
csSpecificity Man page
csSpecificity,CuffData-method Man page
csSpecificity,CuffFeatureSet-method Man page
csVolcano Man page
csVolcano,CuffData-method Man page
csVolcano,CuffFeatureSet-method Man page
csVolcanoMatrix Man page
csVolcanoMatrix,CuffData-method Man page
cummeRbund Man page
cummeRbund-package Man page
diffData Man page
diffData,CuffData-method Man page
diffData,CuffFeature-method Man page
diffData,CuffFeatureSet-method Man page
diffTable Man page
diffTable,CuffData-method Man page
diffTable,CuffFeatureSet-method Man page
dim,CuffData-method Man page
dim,CuffDist-method Man page
dispersionPlot Man page
dispersionPlot,CuffData-method Man page
dispersionPlot,CuffSet-method Man page
distValues Man page
distValues,CuffDist-method Man page
expressionBarplot Man page
expressionBarplot,CuffFeature-method Man page
expressionBarplot,CuffFeatureSet-method Man page
expressionPlot Man page
expressionPlot,CuffFeature-method Man page
expressionPlot,CuffFeatureSet-method Man page
featureNames,CuffData-method Man page
featureNames,CuffFeatureSet-method Man page
features Man page
features,CuffFeatureSet-method Man page
features,CuffGene-method Man page
findGene Man page
findGene,CuffSet-method Man page
findSimilar Man page
findSimilar,CuffSet-method Man page
fpkm Man page
fpkm,CuffData-method Man page
fpkm,CuffFeature-method Man page
fpkm,CuffFeatureSet-method Man page
fpkm-methods Man page
fpkmMatrix Man page
fpkmMatrix,CuffData-method Man page
fpkmMatrix,CuffFeature-method Man page
fpkmMatrix,CuffFeatureSet-method Man page
fpkmSCVPlot Man page
fpkmSCVPlot,CuffData-method Man page
genePlot Man page
genePlot,CuffGene-method Man page
genes Man page
genes,CuffGene-method Man page
genes,CuffGeneSet-method Man page
genes,CuffSet-method Man page
getFeatures Man page
getFeatures,CuffData-method Man page
getFeatures,CuffSet-method Man page
getGene Man page
getGene,CuffSet-method Man page
getGeneId Man page
getGeneId,CuffSet-method Man page
getGenes Man page
getGenes,CuffSet-method Man page
getLevels Man page
getLevels,CuffData-method Man page
getLevels,CuffSet-method Man page
getRepLevels Man page
getRepLevels,CuffData-method Man page
getRepLevels,CuffSet-method Man page
getSamples Source code
getSamplesFromColnames Source code
getSig Man page
getSig,CuffSet-method Man page
getSigTable Man page
getSigTable,CuffSet-method Man page
isoforms Man page
isoforms,CuffGene-method Man page
isoforms,CuffGeneSet-method Man page
isoforms,CuffSet-method Man page
length,CuffFeature-method Man page
length,CuffFeatureSet-method Man page
length,CuffGene-method Man page
loadCDS Source code
loadGenes Source code
loadIsoforms Source code
loadRepTable Source code
loadRunInfo Source code
loadTSS Source code
loadVarModelTable Source code
makeGeneRegionTrack Man page
makeGeneRegionTrack,CuffGene-method Man page
makeRnk Man page
makeRnk,CuffData-method Man page
makeprobs Man page Source code
makeprobsvec Man page Source code
populateSampleTable Source code
promoters Man page
promoters,CuffGene-method Man page
promoters,CuffGeneSet-method Man page
promoters,CuffSet-method Man page
readCufflinks Man page Source code
relCDS Man page
relCDS,CuffGene-method Man page
relCDS,CuffGeneSet-method Man page
relCDS,CuffSet-method Man page
repCountMatrix Man page
repCountMatrix,CuffData-method Man page
repCountMatrix,CuffFeatureSet-method Man page
repFpkm Man page
repFpkm,CuffData-method Man page
repFpkm,CuffFeature-method Man page
repFpkm,CuffFeatureSet-method Man page
repFpkm-methods Man page
repFpkmMatrix Man page
repFpkmMatrix,CuffData-method Man page
repFpkmMatrix,CuffFeature-method Man page
repFpkmMatrix,CuffFeatureSet-method Man page
replicates Man page
replicates,CuffData-method Man page
replicates,CuffFeature-method Man page
replicates,CuffFeatureSet-method Man page
replicates,CuffSet-method Man page
runInfo Man page
runInfo,CuffSet-method Man page
sampleGeneSet Man page
sampleIDs Man page
samples Man page
samples,CuffData-method Man page
samples,CuffDist-method Man page
samples,CuffFeature-method Man page
samples,CuffFeatureSet-method Man page
samples,CuffSet-method Man page
shannon.entropy Man page Source code
sigMatrix Man page
sigMatrix,CuffSet-method Man page
splicing Man page
splicing,CuffGene-method Man page
splicing,CuffGeneSet-method Man page
splicing,CuffSet-method Man page
varModel Man page
varModel,CuffSet-method Man page
cummeRbund documentation built on Nov. 8, 2020, 7:53 p.m.

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