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

Global functions
CDS Man page
CDS,CuffGene-method Man page
CDS,CuffGeneSet-method Man page
CDS,CuffSet-method Man page
CVdensity Source code
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 Source code
MAplot,CuffData-method Man page
MDSplot Man page Source code Source code
MDSplot,CuffData-method Man page
MDSplot,CuffFeatureSet-method Man page
PCAplot Man page Source code Source code
PCAplot,CuffData-method Man page
PCAplot,CuffFeatureSet-method Man page
PINK1 Man page
QCTable Source code
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 Source code Source code
addFeatures,CuffData-method Man page
addFeatures,CuffSet-method Man page
annotation Man page Source code Source code
annotation,CuffData-method Man page
annotation,CuffFeature-method Man page
annotation,CuffFeatureSet-method Man page
as.GRanges Source code
as.GRangesList Source code
barplot Source code Source code
boxplot Source code
bulk_insert Source code
checkReps Source code
checkSamples Source code Source code
cluster Source code
conditions Man page
conditions,CuffSet-method Man page
confidencePlot Source code
count Man page Source code Source code Source code
count,CuffData-method Man page
count,CuffFeature-method Man page
count,CuffFeatureSet-method Man page
count-methods Man page
countMatrix Man page Source code Source code
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 Source code
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
cuff2db Source code
cummeRbund Man page
cummeRbund-package Man page
dendro Source code Source code
density Source code Source code
deogram Source code
dfToJSONarray Source code
diffData Man page Source code Source code Source code
diffData,CuffData-method Man page
diffData,CuffFeature-method Man page
diffData,CuffFeatureSet-method Man page
diffTable Man page Source code Source code
diffTable,CuffData-method Man page
diffTable,CuffFeatureSet-method Man page
dim,CuffData-method Man page
dim,CuffDist-method Man page
dispersionPlot Man page Source code Source code
dispersionPlot,CuffData-method Man page
dispersionPlot,CuffSet-method Man page
distValues Man page
distValues,CuffDist-method Man page
distheat Source code Source code
expressionBarplot Man page
expressionBarplot,CuffFeature-method Man page
expressionBarplot,CuffFeatureSet-method Man page
expressionPlot Man page Source code Source code
expressionPlot,CuffFeature-method Man page
expressionPlot,CuffFeatureSet-method Man page
fcheatmap Source code
featureNames Source code Source code
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 Source code
findGene,CuffSet-method Man page
findK Source code
findSimilar Man page Source code
findSimilar,CuffSet-method Man page
fpkm Man page Source code Source code Source code
fpkm,CuffData-method Man page
fpkm,CuffFeature-method Man page
fpkm,CuffFeatureSet-method Man page
fpkm-methods Man page
fpkmMatrix Man page Source code Source code Source code
fpkmMatrix,CuffData-method Man page
fpkmMatrix,CuffFeature-method Man page
fpkmMatrix,CuffFeatureSet-method Man page
fpkmSCVPlot Man page Source code
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
getCountMA Source code
getFeatures Man page Source code
getFeatures,CuffData-method Man page
getFeatures,CuffSet-method Man page
getGene Man page Source code
getGene,CuffSet-method Man page
getGeneId Man page Source code
getGeneId,CuffSet-method Man page
getGenes Man page Source code
getGenes,CuffSet-method Man page
getGenome Source code
getLevels Man page Source code Source code
getLevels,CuffData-method Man page
getLevels,CuffSet-method Man page
getMA Source code
getRepConditionLevels Source code
getRepLevels Man page Source code Source code
getRepLevels,CuffData-method Man page
getRepLevels,CuffSet-method Man page
getSamples Source code
getSamplesFromColnames Source code
getSig Man page Source code
getSig,CuffSet-method Man page
getSigTable Man page Source code
getSigTable,CuffSet-method Man page
ggheat Source code
hclustToJSON Source code
heatmap Source code
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
loadGTF Source code
loadGenes Source code
loadIsoforms Source code
loadRepTable Source code
loadRunInfo Source code
loadTSS Source code
loadVarModelTable Source code
makeGRanges Source code
makeGeneRegionTrack Man page Source code
makeGeneRegionTrack,CuffGene-method Man page
makeIdentityMatrix Source code
makeRnk Man page Source code
makeRnk,CuffData-method Man page
makeRnkTest Source code
makeRnkTestStat Source code
makeprobs Man page Source code
makeprobsvec Man page Source code
nmf Source code Source code
pie Source code
plot Source code
plot2 Source code
plotmatrix Source code
populateSampleTable Source code
promoters Man page
promoters,CuffGene-method Man page
promoters,CuffGeneSet-method Man page
promoters,CuffSet-method Man page
ratioCluster Source code
readCufflinks Man page Source code
recordGenome Source code
relCDS Man page
relCDS,CuffGene-method Man page
relCDS,CuffGeneSet-method Man page
relCDS,CuffSet-method Man page
repCountMatrix Man page Source code Source code
repCountMatrix,CuffData-method Man page
repCountMatrix,CuffFeatureSet-method Man page
repFpkm Man page Source code Source code Source code
repFpkm,CuffData-method Man page
repFpkm,CuffFeature-method Man page
repFpkm,CuffFeatureSet-method Man page
repFpkm-methods Man page
repFpkmMatrix Man page Source code Source code Source code
repFpkmMatrix,CuffData-method Man page
repFpkmMatrix,CuffFeature-method Man page
repFpkmMatrix,CuffFeatureSet-method Man page
replicates Man page Source code Source code Source code Source code
replicates,CuffData-method Man page
replicates,CuffFeature-method Man page
replicates,CuffFeatureSet-method Man page
replicates,CuffSet-method Man page
runInfo Man page Source code
runInfo,CuffSet-method Man page
sampleGeneSet Man page
sampleIDs Man page
samples Man page Source code Source code Source code Source code Source code
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
scatter Source code Source code
scatter2 Source code
scatterMat Source code
sensitivityPlot Source code
shannon.entropy Man page Source code
sigMatrix Man page Source code
sigMatrix,CuffSet-method Man page
specificity Source code Source code Source code
splicing Man page
splicing,CuffGene-method Man page
splicing,CuffGeneSet-method Man page
splicing,CuffSet-method Man page
statsMatrix Source code
values Source code
varModel Man page Source code
varModel,CuffSet-method Man page
volcano Source code Source code
volcanoMatrix Source code
gofflab/cummeRbund-BioC-Bridge documentation built on May 14, 2017, 1:58 p.m.