ASpli-deprecated        Deprecated functions in package 'ASpli'
ASpli-package           Analysis of Alternative Splicing Using RNAseq
ASpliAS-class           Class '"ASpliAS"'
ASpliCounts             Class '"ASpliCounts"'
ASpliCounts-class       Class '"ASpliCounts"'
ASpliDU-class           Class '"ASpliDU"'
ASpliFeatures-class     Class '"ASpliFeatures"'
ASpliIntegratedSignals-class
                        Class '"ASpliIntegratedSignals"'
ASpliJDU-class          Class '"ASpliJDU"'
ASpliSplicingReport-class
                        Class '"ASpliSplicingReport"'
DUreport                Differential gene expression and differential
                        bin usage estimation
DUreport.norm           Differential gene expression and differential
                        bin usage estimation
DUreport.offset         Differential gene expression and differential
                        bin usage estimation
DUreportBinSplice       Differential gene expression and differential
                        bin usage estimation
altPSI                  Accessors for ASpliAS object
anchorc                 Accessors for ASpliJDU object
aspliASexample          Example Aspli objects
binGenome               Feature coordinates extraction
binGenome-methods       Feature coordinates extraction
binbased                Accessors for ASpliSplicingReport object
containsJunctions       Examine ASpliDU objects
countsb                 Accessors for ASpliCounts object
exportIntegratedSignals
                        Export integrated signals.
exportSplicingReports   Export splicing reports
featuresb               Accessors for ASpliFeatures object
filterDU                Filtering ASpliDU objects
filterSignals           Filter signals
gbCounts                Summarize read overlaps
gbDUreport              Differential gene expression and differential
                        bin usage estimation
genesDE                 Accessors for ASpliDU object
getConditions           Retrieve condition names from a targets data
                        frame.
integrateSignals        Integrate signals
jCounts                 Report PSI, PJU and PIR using experimental
                        junctions
jDUreport               Differential junction usage estimation
junctionDUreport        Differential junction usage estimation
loadBAM                 Load BAM files
mergeBinDUAS            Differential usage of bins and PSI/PIR.
plotBins                Draw plots of gene counts, bin counts, PSI/PIR
                        value, inclusion and exclusion junctions for
                        selected bins.
plotGenomicRegions      Create genomic regions coverage plots
rds                     Read density of gene and bins
show-methods            Display a summary of data contained in
                        ASpliObjects
signals                 Accessors for ASpliIntegratedSignals object
splicingReport          Splicing report
subsetBams              Subset ASpli objects
writeRds                Write results
writeRds-methods        Write results
