ASpli-package	ASpli-package
altPSI	acc_AS
altPSI,ASpliAS-method	ASpliAS-class
altPSI<-	acc_AS
altPSI<-,ASpliAS,data.frame-method	ASpliAS-class
anchorbased	acc_MergedReport
anchorbased,ASpliSplicingReport-method	ASpliSplicingReport-class
anchorbased<-	acc_MergedReport
anchorbased<-,ASpliSplicingReport,data.frame-method	ASpliSplicingReport-class
anchorc	acc_JDU
anchorc,ASpliJDU-method	ASpliJDU-class
anchorc<-	acc_JDU
anchorc<-,ASpliJDU,data.frame-method	ASpliJDU-class
anchorj	acc_JDU
anchorj,ASpliJDU-method	ASpliJDU-class
anchorj<-	acc_JDU
anchorj<-,ASpliJDU,data.frame-method	ASpliJDU-class
AsDiscover	jCounts-methods
AsDiscover,ASpliCounts-method	ASpliCounts-class
ASpli	ASpli-package
ASpli-deprecated	ASpli-deprecated
ASpliAS	ASpliAS-class
ASpliAS-class	ASpliAS-class
aspliASexample	example_data
aspliBamsExample	example_data
ASpliCounts	ASpliCounts
ASpliCounts-class	ASpliCounts-class
aspliCountsExample	example_data
ASpliDU	ASpliDU-class
ASpliDU-class	ASpliDU-class
aspliDUexample1	example_data
aspliDUexample2	example_data
aspliExampleBamList	example_data
aspliExampleGTF	example_data
ASpliFeatures-class	ASpliFeatures-class
aspliFeaturesExample	example_data
ASpliIntegratedSignals	ASpliIntegratedSignals-class
ASpliIntegratedSignals-class	ASpliIntegratedSignals-class
ASpliJDU	ASpliJDU-class
ASpliJDU-class	ASpliJDU-class
aspliJunctionDUexample	example_data
ASpliSplicingReport	ASpliSplicingReport-class
ASpliSplicingReport-class	ASpliSplicingReport-class
aspliTargetsExample	example_data
binbased	acc_MergedReport
binbased,ASpliSplicingReport-method	ASpliSplicingReport-class
binbased<-	acc_MergedReport
binbased<-,ASpliSplicingReport,data.frame-method	ASpliSplicingReport-class
binGenome	binGenome
binGenome,TxDb-method	binGenome-methods
binGenome-methods	binGenome-methods
binsDU	acc_DU
binsDU,ASpliDU-method	ASpliDU-class
binsDU<-	acc_DU
binsDU<-,ASpliDU-method	ASpliDU-class
condition.order	acc_counts
condition.order,ASpliCounts-method	ASpliCounts-class
containsGenesAndBins	containsJunctions-function
containsGenesAndBins,ASpliDU-method	ASpliDU-class
containsJunctions	containsJunctions-function
containsJunctions,ASpliDU-method	ASpliDU-class
countsb	acc_counts
countsb,ASpliCounts-method	ASpliCounts-class
countsb<-	acc_counts
countsb<-,ASpliCounts,data.frame-method	ASpliCounts-class
countse1i	acc_counts
countse1i,ASpliCounts-method	ASpliCounts-class
countse1i<-	acc_counts
countse1i<-,ASpliCounts,data.frame-method	ASpliCounts-class
countsg	acc_counts
countsg,ASpliCounts-method	ASpliCounts-class
countsg<-	acc_counts
countsg<-,ASpliCounts,data.frame-method	ASpliCounts-class
countsie2	acc_counts
countsie2,ASpliCounts-method	ASpliCounts-class
countsie2<-	acc_counts
countsie2<-,ASpliCounts,data.frame-method	ASpliCounts-class
countsj	acc_counts
countsj,ASpliCounts-method	ASpliCounts-class
countsj<-	acc_counts
countsj<-,ASpliCounts,data.frame-method	ASpliCounts-class
DUreport	DUreport
DUreport,ASpliCounts-method	ASpliCounts-class
DUreport.norm	DUreport.norm
DUreport.norm,ASpliCounts-method	ASpliCounts-class
DUreport.offset	DUreport.offset
DUreport.offset,ASpliCounts-method	ASpliCounts-class
DUreportBinSplice	DUreportBinSplice-method
DUreportBinSplice,ASpliCounts-method	ASpliCounts-class
esPSI	acc_AS
esPSI,ASpliAS-method	ASpliAS-class
esPSI<-	acc_AS
esPSI<-,ASpliAS,data.frame-method	ASpliAS-class
exportIntegratedSignals	exportIntegratedSignals
exportIntegratedSignals,ASpliIntegratedSignals-method	ASpliIntegratedSignals-class
exportSplicingReports	exportSplicingReports
exportSplicingReports,ASpliSplicingReport-method	ASpliSplicingReport-class
featuresb	acc_features
featuresb,ASpliFeatures-method	ASpliFeatures-class
featuresb<-	acc_features
featuresb<-,ASpliFeatures,GRanges-method	ASpliFeatures-class
featuresg	acc_features
featuresg,ASpliFeatures-method	ASpliFeatures-class
featuresg<-	acc_features
featuresg<-,ASpliFeatures,GRangesList-method	ASpliFeatures-class
featuresj	acc_features
featuresj,ASpliFeatures-method	ASpliFeatures-class
featuresj<-	acc_features
featuresj<-,ASpliFeatures,GRanges-method	ASpliFeatures-class
filterDU	filterDU-method
filterDU,ASpliDU-method	ASpliDU-class
filters	acc_is
filters,ASpliIntegratedSignals-method	ASpliIntegratedSignals-class
filters<-	acc_is
filters<-,ASpliIntegratedSignals,data.frame-method	ASpliIntegratedSignals-class
filterSignals	filterSignals
filterSignals,ASpliSplicingReport-method	ASpliSplicingReport-class
gbCounts	gbCounts
gbCounts,ASpliFeatures-method	ASpliFeatures-class
gbDUreport	gbDUreport-method
gbDUreport,ASpliCounts-method	ASpliCounts-class
genesDE	acc_DU
genesDE,ASpliDU-method	ASpliDU-class
genesDE<-	acc_DU
genesDE<-,ASpliDU,data.frame-method	ASpliDU-class
getConditions	getConditions-function
integrateSignals	integrateSignals
integrateSignals,ASpliSplicingReport-method	ASpliSplicingReport-class
irPIR	acc_AS
irPIR,ASpliAS-method	ASpliAS-class
irPIR<-	acc_AS
irPIR<-,ASpliAS,data.frame-method	ASpliAS-class
jalt	acc_JDU
jalt,ASpliJDU-method	ASpliJDU-class
jalt<-	acc_JDU
jalt<-,ASpliJDU,data.frame-method	ASpliJDU-class
jCounts	jCounts-methods
jCounts,ASpliCounts-method	ASpliCounts-class
jDUreport	jDUreport
jDUreport,ASpliAS-method	ASpliAS-class
jDUreport,ASpliJDU-method	ASpliJDU-class
jes	acc_JDU
jes,ASpliJDU-method	ASpliJDU-class
jes<-	acc_JDU
jes<-,ASpliJDU,data.frame-method	ASpliJDU-class
jir	acc_JDU
jir,ASpliJDU-method	ASpliJDU-class
jir<-	acc_JDU
jir<-,ASpliJDU,data.frame-method	ASpliJDU-class
joint	acc_AS
joint,ASpliAS-method	ASpliAS-class
joint<-	acc_AS
joint<-,ASpliAS,data.frame-method	ASpliAS-class
junctionDUreport	junctionDUreport
junctionDUreport,ASpliCounts-method	ASpliCounts-class
junctionsDU	acc_DU
junctionsDU,ASpliDU-method	ASpliDU-class
junctionsDU<-	acc_DU
junctionsDU<-,ASpliDU,data.frame-method	ASpliDU-class
junctionsPIR	acc_AS
junctionsPIR,ASpliAS-method	ASpliAS-class
junctionsPIR<-	acc_AS
junctionsPIR<-,ASpliAS,data.frame-method	ASpliAS-class
junctionsPJU	acc_AS
junctionsPJU,ASpliAS-method	ASpliAS-class
junctionsPJU<-	acc_AS
junctionsPJU<-,ASpliAS,data.frame-method	ASpliAS-class
loadBAM	loadBAM
localebased	acc_MergedReport
localebased,ASpliSplicingReport-method	ASpliSplicingReport-class
localebased<-	acc_MergedReport
localebased<-,ASpliSplicingReport,data.frame-method	ASpliSplicingReport-class
localec	acc_JDU
localec,ASpliJDU-method	ASpliJDU-class
localec<-	acc_JDU
localec<-,ASpliJDU,data.frame-method	ASpliJDU-class
localej	acc_JDU
localej,ASpliJDU-method	ASpliJDU-class
localej<-	acc_JDU
localej<-,ASpliJDU,data.frame-method	ASpliJDU-class
mergeBinDUAS	mergeBinDUAS-method
mergeBinDUAS,ASpliDU,ASpliAS-method	ASpliDU-class
plotBins	plotBins
plotBins,ASpliCounts-method	ASpliCounts-class
plotGenomicRegions	plotGenomicRegions
plotGenomicRegions,ASpliFeatures-method	ASpliFeatures-class
rds	rds
rds,ASpliCounts-method	ASpliCounts-class
rdsb	acc_counts
rdsb,ASpliCounts-method	ASpliCounts-class
rdsb<-	acc_counts
rdsb<-,ASpliCounts,data.frame-method	ASpliCounts-class
rdsg	acc_counts
rdsg,ASpliCounts-method	ASpliCounts-class
rdsg<-	acc_counts
rdsg<-,ASpliCounts,data.frame-method	ASpliCounts-class
readCounts	gbCounts
readCounts,ASpliFeatures-method	ASpliFeatures-class
show,ASpliAS-method	show-methods
show,ASpliCounts-method	show-methods
show,ASpliDU-method	show-methods
show,ASpliFeatures-method	show-methods
show,ASpliIntegratedSignals-method	ASpliIntegratedSignals-class
show,ASpliJDU-method	ASpliJDU-class
show,ASpliMergedReports-method	show-methods
show,ASpliSplicingReport-method	ASpliSplicingReport-class
show-methods	show-methods
signals	acc_is
signals,ASpliIntegratedSignals-method	ASpliIntegratedSignals-class
signals<-	acc_is
signals<-,ASpliIntegratedSignals,data.frame-method	ASpliIntegratedSignals-class
splicingReport	splicingReport
splicingReport,ASpliDU-method	ASpliDU-class
splicingReport,ASpliIntegratedSignals-method	ASpliIntegratedSignals-class
splicingReport,ASpliSplicingReport-method	ASpliSplicingReport-class
subset	subset-methods
subset,ASpliAS-method	ASpliAS-class
subset,ASpliCounts-method	ASpliCounts-class
subsetBams	subset-methods
subsetTargets	subset-methods
targets	acc_counts
targets,ASpliCounts-method	ASpliCounts-class
targets<-,ASpliCounts,data.frame-method	ASpliCounts-class
transcriptExons	acc_features
transcriptExons,ASpliFeatures-method	ASpliFeatures-class
transcriptExons<-	acc_features
transcriptExons<-,ASpliFeatures,GRangesList-method	ASpliFeatures-class
writeAll	write
writeAll,ANY-method	write-methods
writeAll,ASpliCounts-method	ASpliCounts-class
writeAS	write
writeAS,ASpliAS-method	ASpliAS-class
writeAS-methods	write-methods
writeCounts	write
writeCounts,ASpliCounts-method	ASpliCounts-class
writeCounts-methods	write-methods
writeDU	write
writeDU,ASpliDU-method	ASpliDU-class
writeDU-methods	write-methods
writeIntegratedSignals,ASpliIntegratedSignals-method	ASpliIntegratedSignals-class
writeJDU	write
writeJDU,ASpliJDU-method	ASpliJDU-class
writeJDU-methods	write-methods
writeRds	write
writeRds,ASpliCounts-method	ASpliCounts-class
writeRds-methods	write-methods
writeSplicingReport	write
writeSplicingReport,ASpliSplicingReport-method	ASpliSplicingReport-class
writeSplicingReport-methods	write-methods
