computeProbs            Function to compute posterior probabilities of
                        modification with the BUM-HMM model for all
                        nucleotides.
computeStretches        Function to compute continuous stretches of
                        nucleotide positions.
covFile                 Example coverage data set.
docFile                 Example drop-off count data set.
dorFile                 Example drop-off rate data set.
findPatternPos          Function to find positions of the nucleotide
                        patterns in the sequence.
nuclPerm                Function to create nucleobase patterns.
scaleDOR                Function to scale drop-off rates across
                        replicates to a common median.
se                      Example RNA structure probing data set.
selectNuclPos           Function to compute selections of nucleotide
                        positions.
seq                     Example genomic sequence string.
stabiliseVariance       Function to reduce variance of LDRs as a
                        function of coverage.
