SGFeatureCounts         Constructor function for S4 class
                        'SGFeatureCounts'
SGFeatures              Constructor function for S4 class 'SGFeatures'
TxFeatures              Constructor function for S4 class 'TxFeatures'
TxVariantCounts         Constructor function for S4 class
                        'SGFeatureCounts'
TxVariants              Constructor function for S4 class 'TxVariants'
analyzeFeatures         Analysis of splice graph features from BAM
                        files
analyzeVariants         Analysis of transcript variants
annotate                Annotation with respect to transcript features
assays                  Accessing and replacing assay data
convertToSGFeatures     Convert transcript features to splice graph
                        features
convertToTxFeatures     Convert to TxFeatures object
exportFeatures          Export to BED format
filterTerminalExons     Filter terminal exons that share splice sites
                        with internal exons
findTxVariants          Find transcript variants from splice graph
getBamInfo              Obtain alignment information from BAM files
getSGFeatureCounts      Compatible counts for splice graph features
                        from BAM files
getTxVariantCounts      Representative counts and frequency estimates
                        for transcript variants
mergeTxFeatures         Merge redundant features
plotFeatures            Plot splice graph and heatmap of expression
                        values
plotSpliceGraph         Plot splice graph
plotVariants            Plot splice graph and heatmap of variant
                        frequencies
predictTxFeatures       Transcript feature prediction from BAM files
slots                   Accessing and replacing column slots
