API for ASpli
Analysis of alternative splicing using RNA-Seq

Global functions
ASpli Man page
ASpli-package Man page
ASpliAS Man page
ASpliAS-class Man page
ASpliCounts Man page
ASpliCounts-class Man page
ASpliDU Man page
ASpliDU-class Man page
ASpliFeatures-class Man page
AsDiscover Man page
AsDiscover,ASpliCounts-method Man page
DUReportBins Source code
DUReportBinsWithDiffSplice Source code
DUreport Man page Source code
DUreport,ASpliCounts-method Man page
DUreportBinSplice Man page Source code
DUreportBinSplice,ASpliCounts-method Man page
DUreportGenes Source code
altPSI Man page
altPSI,ASpliAS-method Man page
altPSI<- Man page
altPSI<-,ASpliAS,data.frame-method Man page
arrangeLayout Source code
aspliASexample Man page Source code
aspliBamsExample Man page Source code
aspliCountsExample Man page Source code
aspliDUexample1 Man page Source code
aspliDUexample2 Man page Source code
aspliExampleBamList Man page Source code
aspliExampleGTF Man page Source code
aspliFeaturesExample Man page Source code
aspliJunctionDUexample Man page Source code
aspliTargetsExample Man page Source code
binGenome Man page
binGenome,TxDb-method Man page
binGenome-methods Man page
binsDU Man page Source code
binsDU,ASpliDU-method Man page
binsDU<- Man page
binsDU<-,ASpliDU-method Man page
binsDUWithDiffSplice Source code
condenseTargetsConditions Source code
containsGenesAndBins Man page
containsGenesAndBins,ASpliDU-method Man page
containsJunctions Man page
containsJunctions,ASpliDU-method Man page
counterBin Source code
counterGenes Source code
counterJbin Source code
counterJunctions Source code
countsb Man page
countsb,ASpliCounts-method Man page
countsb<- Man page
countsb<-,ASpliCounts,data.frame-method Man page
countse1i Man page
countse1i,ASpliCounts-method Man page
countse1i<- Man page
countse1i<-,ASpliCounts,data.frame-method Man page
countsg Man page
countsg,ASpliCounts-method Man page
countsg<- Man page
countsg<-,ASpliCounts,data.frame-method Man page
countsie2 Man page
countsie2,ASpliCounts-method Man page
countsie2<- Man page
countsie2<-,ASpliCounts,data.frame-method Man page
countsj Man page
countsj,ASpliCounts-method Man page
countsj<- Man page
countsj<-,ASpliCounts,data.frame-method Man page
createGRangesExons Source code
createGRangesExons.getExonBinNames Source code
createGRangesExons.getExonBins Source code
createGRangesExons.getExonsFromMultiExonicGenes Source code
createGRangesExpJunctions Source code
createGRangesGenes Source code
createGRangesGenes.getGeneCoordinates Source code
createGRangesGenes.getGeneCoordinates.old Source code
createGRangesGenes.getLocusOverlap Source code
createGRangesIntrons Source code
createGRangesJunctions Source code
createGRangesJunctions.getJunctions Source code
createGRangesJunctions.getUniqueIntrons Source code
createGRangesJunctions.intronsByGene Source code
createGRangesTranscripts Source code
definePlottingRegions Source code
e2JPIR Source code
edgeRtest Source code
esPSI Man page
esPSI,ASpliAS-method Man page
esPSI<- Man page
esPSI<-,ASpliAS,data.frame-method Man page
evaluateByGroup Source code
extractCountColumns Source code
extractDataColumns Source code
extractValuesToFilter Source code
featuresb Man page
featuresb,ASpliFeatures-method Man page
featuresb<- Man page
featuresb<-,ASpliFeatures,GRanges-method Man page
featuresg Man page
featuresg,ASpliFeatures-method Man page
featuresg<- Man page
featuresg<-,ASpliFeatures,GRangesList-method Man page
featuresj Man page
featuresj,ASpliFeatures-method Man page
featuresj<- Man page
featuresj<-,ASpliFeatures,GRanges-method Man page
filter.ASpliDU Source code
filterBins Source code
filterByGeneric Source code
filterByGroup Source code
filterByRdBinRATIO Source code
filterByRdGen Source code
filterByReads Source code
filterDU Man page
filterDU,ASpliDU-method Man page
filterGenes Source code
filterJunctionBySample Source code
filterReadCounts Source code
findAsBin Source code
genesDE Man page Source code
genesDE,ASpliDU-method Man page
genesDE<- Man page
genesDE<-,ASpliDU,data.frame-method Man page
getBamMatrix Source code
getConditions Man page Source code
getDefaultContrasts Source code
getExpFactors Source code
getFilteringConditions Source code
getHCColor Source code
getJPSIByOverlap Source code
getOffsetMatrix Source code
irPIR Man page
irPIR,ASpliAS-method Man page
irPIR<- Man page
irPIR<-,ASpliAS,data.frame-method Man page
joint Man page
joint,ASpliAS-method Man page
joint<- Man page
joint<-,ASpliAS,data.frame-method Man page
junctionDUreport Man page Source code
junctionDUreport,ASpliCounts-method Man page
junctionsDU Man page
junctionsDU,ASpliDU-method Man page
junctionsDU<- Man page
junctionsDU<-,ASpliDU,data.frame-method Man page
junctionsDU_SUM Source code
junctionsDiscover Source code
junctionsPIR Man page
junctionsPIR,ASpliAS-method Man page
junctionsPIR<- Man page
junctionsPIR<-,ASpliAS,data.frame-method Man page
junctionsPSI Man page
junctionsPSI,ASpliAS-method Man page
junctionsPSI<- Man page
junctionsPSI<-,ASpliAS,data.frame-method Man page
junctionsPSI_SUM Source code
loadASpliObject Source code
loadBAM Man page Source code
makeGenomeRegionPlot Source code
makeLegends Source code
makePlot Source code
makeValidFileName Source code
makeXticksLabels Source code
mergeBamsByCondition Source code
mergeBinDUAS Man page Source code
mergeBinDUAS,ASpliDU,ASpliAS-method Man page
normalizeByGenFeature Source code
ovBinJunction Source code
plotBars Source code
plotBins Man page Source code
plotBins,ASpliCounts-method Man page
plotGenomicRegions Man page Source code
plotGenomicRegions,ASpliFeatures-method Man page
plotLines Source code
plotSingleBin Source code
prepareData Source code
rds Man page
rds,ASpliCounts-method Man page
rdsb Man page
rdsb,ASpliCounts-method Man page
rdsb<- Man page
rdsb<-,ASpliCounts,data.frame-method Man page
rdsg Man page
rdsg,ASpliCounts-method Man page
rdsg<- Man page
rdsg<-,ASpliCounts,data.frame-method Man page
readCounts Man page
readCounts,ASpliFeatures-method Man page
rowMin Source code
setDefaultOffsets Source code
shiftVector Source code
show,ASpliAS-method Man page
show,ASpliCounts-method Man page
show,ASpliDU-method Man page
show,ASpliFeatures-method Man page
show-methods Man page
subset Man page
subset,ASpliAS-method Man page
subset,ASpliCounts-method Man page
subset.ASpliAS Source code
subset.ASpliCounts Source code
subsetBams Man page Source code
subsetTargets Man page Source code
sumByCond Source code
vecMin Source code
writeAS Man page
writeAS,ASpliAS-method Man page
writeAS-methods Man page
writeAll Man page
writeAll,ANY-method Man page
writeAll,ASpliCounts-method Man page
writeCounts Man page
writeCounts,ASpliCounts-method Man page
writeCounts-methods Man page
writeDU Man page
writeDU,ASpliDU-method Man page
writeDU-methods Man page
writeRds Man page
writeRds,ASpliCounts-method Man page
writeRds-methods Man page
ASpli documentation built on Nov. 17, 2017, 8:26 a.m.