chernolab/ASpli
Analysis of Alternative Splicing Using RNA-Seq

Package index
Search the chernolab/ASpli package
Functions
337
Source code
21
Man pages
46
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chernolab/ASpli: Analysis of Alternative Splicing Using RNA-Seq
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API

API for chernolab/ASpli
Analysis of Alternative Splicing Using RNA-Seq

Global functions
.DUReportBins Source code
.DUReportBinsWithDiffSplice Source code
.DUreport Source code
.arrangeLayout Source code
.binsDUWithDiffSplice Source code
.binsJDUWithDiffSplice Source code
.countJbyCondition Source code
.counterBin Source code
.counterGenes Source code
.counterJbin Source code
.counterJunctions Source code
.createGRangesExons Source code
.createGRangesExpJunctions Source code
.createGRangesGenes Source code
.createGRangesIntrons Source code
.createGRangesJunctions Source code
.createGRangesTranscripts Source code
.definePlottingRegions Source code
.e1e2JPIR Source code
.edgeRtest Source code
.evaluateByGroup Source code
.filter.ASpliDU Source code
.filterBins Source code
.filterByGeneric Source code
.filterByGroup Source code
.filterByRdBinRATIO Source code
.filterByRdGen Source code
.filterByReads Source code
.filterGenes Source code
.filterJunctionBySample Source code
.filterJunctionBySampleWithContrast Source code
.filterReadCounts Source code
.filterSignals Source code
.findAsBin Source code
.genesDE Source code
.getBamMatrix Source code
.getExpFactors Source code
.getGeneGRanges Source code
.getJunctionMatchingBins Source code
.getJunctionOverlapGeneData Source code
.getJunctionSpanningBins Source code
.getJunctionWithinBins Source code
.getOffsetMatrix Source code
.integrateSignals Source code
.junctionDUreportExt Source code
.junctionsDU_SUM Source code
.junctionsDiscover Source code
.junctionsPSI_SUM Source code
.makeClusters Source code
.makeCountData Source code
.makeCountDataWithClusters Source code
.makeJunctions Source code
.makeLegends Source code
.makeReduxData Source code
.makeValidFileName Source code
.makeXticksLabels Source code
.meanLogCPMIs Source code
.mergeBinDUAS Source code
.my_replace_na Source code
.normalizeByGenFeature Source code
.ovBinJunction Source code
.plotASpliDetectionSummary Source code
.plotBars Source code
.plotBins Source code
.plotGenomicRegions Source code
.plotSingleBin Source code
.plotSplicingPattern Source code
.plotSplicingPattern.orig Source code
.prepareData Source code
.splicingReport Source code
.subset.ASpliAS Source code
.subset.ASpliCounts Source code
.sumByCond Source code
.testUniformity Source code
ASpli Man page
ASpli-deprecated 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
ASpliIntegratedSignals Man page
ASpliIntegratedSignals-class Man page
ASpliJDU Man page
ASpliJDU-class Man page
ASpliSplicingReport Man page
ASpliSplicingReport-class Man page
AsDiscover Man page
AsDiscover,ASpliCounts-method Man page
DUreport Man page
DUreport,ASpliCounts-method Man page
DUreport.norm Man page
DUreport.norm,ASpliCounts-method Man page
DUreport.offset Man page
DUreport.offset,ASpliCounts-method Man page
DUreportBinSplice Man page
DUreportBinSplice,ASpliCounts-method Man page
altPSI Man page
altPSI,ASpliAS-method Man page
altPSI<- Man page
altPSI<-,ASpliAS,data.frame-method Man page
anchorbased Man page
anchorbased,ASpliSplicingReport-method Man page
anchorbased<- Man page
anchorbased<-,ASpliSplicingReport,data.frame-method Man page
anchorc Man page
anchorc,ASpliJDU-method Man page
anchorc<- Man page
anchorc<-,ASpliJDU,data.frame-method Man page
anchorj Man page
anchorj,ASpliJDU-method Man page
anchorj<- Man page
anchorj<-,ASpliJDU,data.frame-method Man page
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
binbased Man page
binbased,ASpliSplicingReport-method Man page
binbased<- Man page
binbased<-,ASpliSplicingReport,data.frame-method Man page
binsDU Man page
binsDU,ASpliDU-method Man page
binsDU<- Man page
binsDU<-,ASpliDU-method Man page
condition.order Man page
condition.order,ASpliCounts-method Man page
containsGenesAndBins Man page
containsGenesAndBins,ASpliDU-method Man page
containsJunctions Man page
containsJunctions,ASpliDU-method Man page
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
esPSI Man page
esPSI,ASpliAS-method Man page
esPSI<- Man page
esPSI<-,ASpliAS,data.frame-method Man page
exportIntegratedSignals Man page
exportIntegratedSignals,ASpliIntegratedSignals-method Man page
exportSplicingReports Man page
exportSplicingReports,ASpliSplicingReport-method Man page
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
filterDU Man page
filterDU,ASpliDU-method Man page
filterSignals Man page
filterSignals,ASpliSplicingReport-method Man page
filters Man page
filters,ASpliIntegratedSignals-method Man page
filters<- Man page
filters<-,ASpliIntegratedSignals,data.frame-method Man page
gbCounts Man page
gbCounts,ASpliFeatures-method Man page
gbDUreport Man page
gbDUreport,ASpliCounts-method Man page
genesDE Man page
genesDE,ASpliDU-method Man page
genesDE<- Man page
genesDE<-,ASpliDU,data.frame-method Man page
getConditions Man page Source code
integrateSignals Man page
integrateSignals,ASpliSplicingReport-method Man page
irPIR Man page
irPIR,ASpliAS-method Man page
irPIR<- Man page
irPIR<-,ASpliAS,data.frame-method Man page
jCounts Man page
jCounts,ASpliCounts-method Man page
jDUreport Man page
jDUreport,ASpliAS-method Man page
jDUreport,ASpliJDU-method Man page
jalt Man page
jalt,ASpliJDU-method Man page
jalt<- Man page
jalt<-,ASpliJDU,data.frame-method Man page
jes Man page
jes,ASpliJDU-method Man page
jes<- Man page
jes<-,ASpliJDU,data.frame-method Man page
jir Man page
jir,ASpliJDU-method Man page
jir<- Man page
jir<-,ASpliJDU,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
junctionDUreport,ASpliCounts-method Man page
junctionsDU Man page
junctionsDU,ASpliDU-method Man page
junctionsDU<- Man page
junctionsDU<-,ASpliDU,data.frame-method Man page
junctionsPIR Man page
junctionsPIR,ASpliAS-method Man page
junctionsPIR<- Man page
junctionsPIR<-,ASpliAS,data.frame-method Man page
junctionsPJU Man page
junctionsPJU,ASpliAS-method Man page
junctionsPJU<- Man page
junctionsPJU<-,ASpliAS,data.frame-method Man page
loadBAM Man page Source code
localebased Man page
localebased,ASpliSplicingReport-method Man page
localebased<- Man page
localebased<-,ASpliSplicingReport,data.frame-method Man page
localec Man page
localec,ASpliJDU-method Man page
localec<- Man page
localec<-,ASpliJDU,data.frame-method Man page
localej Man page
localej,ASpliJDU-method Man page
localej<- Man page
localej<-,ASpliJDU,data.frame-method Man page
mergeBinDUAS Man page
mergeBinDUAS,ASpliDU,ASpliAS-method Man page
plotBins Man page
plotBins,ASpliCounts-method Man page
plotGenomicRegions Man page
plotGenomicRegions,ASpliFeatures-method Man page
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
show,ASpliAS-method Man page
show,ASpliCounts-method Man page
show,ASpliDU-method Man page
show,ASpliFeatures-method Man page
show,ASpliIntegratedSignals-method Man page
show,ASpliJDU-method Man page
show,ASpliMergedReports-method Man page
show,ASpliSplicingReport-method Man page
show-methods Man page
signals Man page
signals,ASpliIntegratedSignals-method Man page
signals<- Man page
signals<-,ASpliIntegratedSignals,data.frame-method Man page
splicingReport Man page
splicingReport,ASpliDU-method Man page
splicingReport,ASpliIntegratedSignals-method Man page
splicingReport,ASpliSplicingReport-method Man page
subset Man page
subset,ASpliAS-method Man page
subset,ASpliCounts-method Man page
subsetBams Man page Source code
subsetTargets Man page Source code
targets Man page
targets,ASpliCounts-method Man page
targets<-,ASpliCounts,data.frame-method Man page
transcriptExons Man page
transcriptExons,ASpliFeatures-method Man page
transcriptExons<- Man page
transcriptExons<-,ASpliFeatures,GRangesList-method Man page
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
writeIntegratedSignals,ASpliIntegratedSignals-method Man page
writeJDU Man page
writeJDU,ASpliJDU-method Man page
writeJDU-methods Man page
writeRds Man page
writeRds,ASpliCounts-method Man page
writeRds-methods Man page
writeSplicingReport Man page
writeSplicingReport,ASpliSplicingReport-method Man page
writeSplicingReport-methods Man page
chernolab/ASpli documentation built on March 11, 2021, 12:24 a.m.

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