alpine-package          alpine: bias corrected transcript abundance
                        estimation
buildFragtypes          Build fragment types from exons
estimateAbundance       Estimate bias-corrected transcript abundances
                        (FPKM)
extractAlpine           Extract results from estimateAbundance run
                        across genes
fitBiasModels           Fit bias models over single-isoform genes
getFragmentWidths       Get fragment widths
getReadLength           Get read length
mergeGenes              Merge overlapping "genes" into gene clusters
normalizeDESeq          DESeq median ratio normalization for matrix
plotFragLen             Plot fragment length distribution over samples
plotGC                  Plot the fragment GC bias over samples
plotGRL                 Simple segments plot for GRangesList
plotOrder0              Plot parameters of the variable length Markov
                        model (VLMM) for read starts
plotRelPos              Plot relative position bias over samples
predictCoverage         Predict coverage for a single-isoform gene
preprocessedData        Preprocessed data for vignettes and examples
splitGenesAcrossChroms
                        Split genes that have isoforms across
                        chromosomes
splitLongGenes          Split very long genes
