Analysis of Alternative Splicing Using RNA-Seq
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Documentation for package ‘ASpli’ version 2.19.0
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A B C D E F G I J L M P R S T W
| ASpli-package | Analysis of Alternative Splicing Using RNAseq |
-- A --
| altPSI | Accessors for ASpliAS object |
| altPSI-method | Class '"ASpliAS"' |
| altPSI<- | Accessors for ASpliAS object |
| altPSI<--method | Class '"ASpliAS"' |
| anchorbased | Accessors for ASpliSplicingReport object |
| anchorbased-method | Class '"ASpliSplicingReport"' |
| anchorbased<- | Accessors for ASpliSplicingReport object |
| anchorbased<--method | Class '"ASpliSplicingReport"' |
| anchorc | Accessors for ASpliJDU object |
| anchorc-method | Class '"ASpliJDU"' |
| anchorc<- | Accessors for ASpliJDU object |
| anchorc<--method | Class '"ASpliJDU"' |
| anchorj | Accessors for ASpliJDU object |
| anchorj-method | Class '"ASpliJDU"' |
| anchorj<- | Accessors for ASpliJDU object |
| anchorj<--method | Class '"ASpliJDU"' |
| AsDiscover | Report PSI, PJU and PIR using experimental junctions |
| AsDiscover-method | Class '"ASpliCounts"' |
| ASpli | Analysis of Alternative Splicing Using RNAseq |
| ASpli-deprecated | Deprecated functions in package 'ASpli' |
| ASpliAS | Class '"ASpliAS"' |
| ASpliAS-class | Class '"ASpliAS"' |
| aspliASexample | Example Aspli objects |
| aspliBamsExample | Example Aspli objects |
| ASpliCounts | Class '"ASpliCounts"' |
| ASpliCounts-class | Class '"ASpliCounts"' |
| aspliCountsExample | Example Aspli objects |
| ASpliDU | Class '"ASpliDU"' |
| ASpliDU-class | Class '"ASpliDU"' |
| aspliDUexample1 | Example Aspli objects |
| aspliDUexample2 | Example Aspli objects |
| aspliExampleBamList | Example Aspli objects |
| aspliExampleGTF | Example Aspli objects |
| ASpliFeatures-class | Class '"ASpliFeatures"' |
| aspliFeaturesExample | Example Aspli objects |
| ASpliIntegratedSignals | Class '"ASpliIntegratedSignals"' |
| ASpliIntegratedSignals-class | Class '"ASpliIntegratedSignals"' |
| ASpliJDU | Class '"ASpliJDU"' |
| ASpliJDU-class | Class '"ASpliJDU"' |
| aspliJunctionDUexample | Example Aspli objects |
| ASpliSplicingReport | Class '"ASpliSplicingReport"' |
| ASpliSplicingReport-class | Class '"ASpliSplicingReport"' |
| aspliTargetsExample | Example Aspli objects |
-- B --
| binbased | Accessors for ASpliSplicingReport object |
| binbased-method | Class '"ASpliSplicingReport"' |
| binbased<- | Accessors for ASpliSplicingReport object |
| binbased<--method | Class '"ASpliSplicingReport"' |
| binGenome | Feature coordinates extraction |
| binGenome-method | Feature coordinates extraction |
| binGenome-methods | Feature coordinates extraction |
| binsDU | Accessors for ASpliDU object |
| binsDU-method | Class '"ASpliDU"' |
| binsDU<- | Accessors for ASpliDU object |
| binsDU<--method | Class '"ASpliDU"' |
-- C --
| condition.order | Accessors for ASpliCounts object |
| condition.order-method | Class '"ASpliCounts"' |
| containsGenesAndBins | Examine ASpliDU objects |
| containsGenesAndBins-method | Class '"ASpliDU"' |
| containsJunctions | Examine ASpliDU objects |
| containsJunctions-method | Class '"ASpliDU"' |
| countsb | Accessors for ASpliCounts object |
| countsb-method | Class '"ASpliCounts"' |
| countsb<- | Accessors for ASpliCounts object |
| countsb<--method | Class '"ASpliCounts"' |
| countse1i | Accessors for ASpliCounts object |
| countse1i-method | Class '"ASpliCounts"' |
| countse1i<- | Accessors for ASpliCounts object |
| countse1i<--method | Class '"ASpliCounts"' |
| countsg | Accessors for ASpliCounts object |
| countsg-method | Class '"ASpliCounts"' |
| countsg<- | Accessors for ASpliCounts object |
| countsg<--method | Class '"ASpliCounts"' |
| countsie2 | Accessors for ASpliCounts object |
| countsie2-method | Class '"ASpliCounts"' |
| countsie2<- | Accessors for ASpliCounts object |
| countsie2<--method | Class '"ASpliCounts"' |
| countsj | Accessors for ASpliCounts object |
| countsj-method | Class '"ASpliCounts"' |
| countsj<- | Accessors for ASpliCounts object |
| countsj<--method | Class '"ASpliCounts"' |
-- D --
| DUreport | Differential gene expression and differential bin usage estimation |
| DUreport-method | Class '"ASpliCounts"' |
| DUreport.norm | Differential gene expression and differential bin usage estimation |
| DUreport.norm-method | Class '"ASpliCounts"' |
| DUreport.offset | Differential gene expression and differential bin usage estimation |
| DUreport.offset-method | Class '"ASpliCounts"' |
| DUreportBinSplice | Differential gene expression and differential bin usage estimation |
| DUreportBinSplice-method | Class '"ASpliCounts"' |
-- E --
| esPSI | Accessors for ASpliAS object |
| esPSI-method | Class '"ASpliAS"' |
| esPSI<- | Accessors for ASpliAS object |
| esPSI<--method | Class '"ASpliAS"' |
| exportIntegratedSignals | Export integrated signals. |
| exportIntegratedSignals-method | Class '"ASpliIntegratedSignals"' |
| exportSplicingReports | Export splicing reports |
| exportSplicingReports-method | Class '"ASpliSplicingReport"' |
-- F --
| featuresb | Accessors for ASpliFeatures object |
| featuresb-method | Class '"ASpliFeatures"' |
| featuresb<- | Accessors for ASpliFeatures object |
| featuresb<--method | Class '"ASpliFeatures"' |
| featuresg | Accessors for ASpliFeatures object |
| featuresg-method | Class '"ASpliFeatures"' |
| featuresg<- | Accessors for ASpliFeatures object |
| featuresg<--method | Class '"ASpliFeatures"' |
| featuresj | Accessors for ASpliFeatures object |
| featuresj-method | Class '"ASpliFeatures"' |
| featuresj<- | Accessors for ASpliFeatures object |
| featuresj<--method | Class '"ASpliFeatures"' |
| filterDU | Filtering ASpliDU objects |
| filterDU-method | Class '"ASpliDU"' |
| filters | Accessors for ASpliIntegratedSignals object |
| filters-method | Class '"ASpliIntegratedSignals"' |
| filters<- | Accessors for ASpliIntegratedSignals object |
| filters<--method | Class '"ASpliIntegratedSignals"' |
| filterSignals | Filter signals |
| filterSignals-method | Class '"ASpliSplicingReport"' |
-- G --
| gbCounts | Summarize read overlaps |
| gbCounts-method | Class '"ASpliFeatures"' |
| gbDUreport | Differential gene expression and differential bin usage estimation |
| gbDUreport-method | Class '"ASpliCounts"' |
| genesDE | Accessors for ASpliDU object |
| genesDE-method | Class '"ASpliDU"' |
| genesDE<- | Accessors for ASpliDU object |
| genesDE<--method | Class '"ASpliDU"' |
| getConditions | Retrieve condition names from a targets data frame. |
-- I --
| integrateSignals | Integrate signals |
| integrateSignals-method | Class '"ASpliSplicingReport"' |
| irPIR | Accessors for ASpliAS object |
| irPIR-method | Class '"ASpliAS"' |
| irPIR<- | Accessors for ASpliAS object |
| irPIR<--method | Class '"ASpliAS"' |
-- J --
| jalt | Accessors for ASpliJDU object |
| jalt-method | Class '"ASpliJDU"' |
| jalt<- | Accessors for ASpliJDU object |
| jalt<--method | Class '"ASpliJDU"' |
| jCounts | Report PSI, PJU and PIR using experimental junctions |
| jCounts-method | Class '"ASpliCounts"' |
| jDUreport | Differential junction usage estimation |
| jDUreport-method | Class '"ASpliAS"' |
| jDUreport-method | Class '"ASpliJDU"' |
| jes | Accessors for ASpliJDU object |
| jes-method | Class '"ASpliJDU"' |
| jes<- | Accessors for ASpliJDU object |
| jes<--method | Class '"ASpliJDU"' |
| jir | Accessors for ASpliJDU object |
| jir-method | Class '"ASpliJDU"' |
| jir<- | Accessors for ASpliJDU object |
| jir<--method | Class '"ASpliJDU"' |
| joint | Accessors for ASpliAS object |
| joint-method | Class '"ASpliAS"' |
| joint<- | Accessors for ASpliAS object |
| joint<--method | Class '"ASpliAS"' |
| junctionDUreport | Differential junction usage estimation |
| junctionDUreport-method | Class '"ASpliCounts"' |
| junctionsDU | Accessors for ASpliDU object |
| junctionsDU-method | Class '"ASpliDU"' |
| junctionsDU<- | Accessors for ASpliDU object |
| junctionsDU<--method | Class '"ASpliDU"' |
| junctionsPIR | Accessors for ASpliAS object |
| junctionsPIR-method | Class '"ASpliAS"' |
| junctionsPIR<- | Accessors for ASpliAS object |
| junctionsPIR<--method | Class '"ASpliAS"' |
| junctionsPJU | Accessors for ASpliAS object |
| junctionsPJU-method | Class '"ASpliAS"' |
| junctionsPJU<- | Accessors for ASpliAS object |
| junctionsPJU<--method | Class '"ASpliAS"' |
-- L --
| loadBAM | Load BAM files |
| localebased | Accessors for ASpliSplicingReport object |
| localebased-method | Class '"ASpliSplicingReport"' |
| localebased<- | Accessors for ASpliSplicingReport object |
| localebased<--method | Class '"ASpliSplicingReport"' |
| localec | Accessors for ASpliJDU object |
| localec-method | Class '"ASpliJDU"' |
| localec<- | Accessors for ASpliJDU object |
| localec<--method | Class '"ASpliJDU"' |
| localej | Accessors for ASpliJDU object |
| localej-method | Class '"ASpliJDU"' |
| localej<- | Accessors for ASpliJDU object |
| localej<--method | Class '"ASpliJDU"' |
-- M --
| mergeBinDUAS | Differential usage of bins and PSI/PIR. |
| mergeBinDUAS-method | Class '"ASpliDU"' |
-- P --
| plotBins | Draw plots of gene counts, bin counts, PSI/PIR value, inclusion and exclusion junctions for selected bins. |
| plotBins-method | Class '"ASpliCounts"' |
| plotGenomicRegions | Create genomic regions coverage plots |
| plotGenomicRegions-method | Class '"ASpliFeatures"' |
-- R --
| rds | Read density of gene and bins |
| rds-method | Class '"ASpliCounts"' |
| rdsb | Accessors for ASpliCounts object |
| rdsb-method | Class '"ASpliCounts"' |
| rdsb<- | Accessors for ASpliCounts object |
| rdsb<--method | Class '"ASpliCounts"' |
| rdsg | Accessors for ASpliCounts object |
| rdsg-method | Class '"ASpliCounts"' |
| rdsg<- | Accessors for ASpliCounts object |
| rdsg<--method | Class '"ASpliCounts"' |
| readCounts | Summarize read overlaps |
| readCounts-method | Class '"ASpliFeatures"' |
-- S --
| show-method | Class '"ASpliIntegratedSignals"' |
| show-method | Class '"ASpliJDU"' |
| show-method | Class '"ASpliSplicingReport"' |
| show-method | Display a summary of data contained in ASpliObjects |
| show-methods | Display a summary of data contained in ASpliObjects |
| signals | Accessors for ASpliIntegratedSignals object |
| signals-method | Class '"ASpliIntegratedSignals"' |
| signals<- | Accessors for ASpliIntegratedSignals object |
| signals<--method | Class '"ASpliIntegratedSignals"' |
| splicingReport | Splicing report |
| splicingReport-method | Class '"ASpliDU"' |
| splicingReport-method | Class '"ASpliIntegratedSignals"' |
| splicingReport-method | Class '"ASpliSplicingReport"' |
| subset | Subset ASpli objects |
| subset-method | Class '"ASpliAS"' |
| subset-method | Class '"ASpliCounts"' |
| subsetBams | Subset ASpli objects |
| subsetTargets | Subset ASpli objects |
-- T --
| targets | Accessors for ASpliCounts object |
| targets-method | Class '"ASpliCounts"' |
| targets<--method | Class '"ASpliCounts"' |
| transcriptExons | Accessors for ASpliFeatures object |
| transcriptExons-method | Class '"ASpliFeatures"' |
| transcriptExons<- | Accessors for ASpliFeatures object |
| transcriptExons<--method | Class '"ASpliFeatures"' |
-- W --
| writeAll | Write results |
| writeAll-method | Class '"ASpliCounts"' |
| writeAll-method | Write results |
| writeAS | Write results |
| writeAS-method | Class '"ASpliAS"' |
| writeAS-methods | Write results |
| writeCounts | Write results |
| writeCounts-method | Class '"ASpliCounts"' |
| writeCounts-methods | Write results |
| writeDU | Write results |
| writeDU-method | Class '"ASpliDU"' |
| writeDU-methods | Write results |
| writeIntegratedSignals-method | Class '"ASpliIntegratedSignals"' |
| writeJDU | Write results |
| writeJDU-method | Class '"ASpliJDU"' |
| writeJDU-methods | Write results |
| writeRds | Write results |
| writeRds-method | Class '"ASpliCounts"' |
| writeRds-methods | Write results |
| writeSplicingReport | Write results |
| writeSplicingReport-method | Class '"ASpliSplicingReport"' |
| writeSplicingReport-methods | Write results |