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"'
AsDiscover              Report PSI and PIR using experimental junctions
DUreport                Differential gene expression and differential
                        bin usage estimation
DUreportBinSplice       Differential gene expression and differential
                        bin usage estimation
altPSI                  Accessors for ASpliAS object
aspliASexample          Example Aspli objects
binGenome               Feature coordinates extraction
binGenome-methods       Feature coordinates extraction
containsJunctions       Examine ASpliDU objects
countsb                 Accessors for ASpliCounts object
featuresb               Accessors for ASpliFeatures object
filterDU                Filtering ASpliDU objects
genesDE                 Accessors for ASpliDU object
getConditions           Retrieve condition names from a targets data
                        frame.
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
readCounts              Summarize read overlaps
show-methods            Display a summary of data contained in
                        ASpliObjects
subsetBams              Subset ASpli objects
writeRds                Write results
writeRds-methods        Write results
