findPairedBases         Determines paired bases from secondary
                        structure string
flattenDotBracket       Converts an extended Dot-Bracket secondary
                        structure to basic Dot-Bracket notation
generatePairsProbabilityMatrix
                        Generates a matrix of base pair probabilities
pairsToSecondaryStructure
                        Generates a string with the secondary structure
                        of an RNA sequence
plotCompositePairsMatrix
                        Plots a composite matrix of base pair
                        probabilities and paired bases
plotPairsProbabilityMatrix
                        Plots a matrix of base pair probabilities
predictAlternativeSecondaryStructures
                        Predicts alternative secondary structures of a
                        given RNA sequence
predictSecondaryStructure
                        Predicts the secondary structure of a given RNA
                        sequence
readCT                  Reads a file with the secondary structure of an
                        RNA in the CT format
readDotBracket          Reads a file with the sequence and secondary
                        structure of an RNA in the Dot-Bracket format
rnaCentralGenomicCoordinatesSearch
                        Retrieves annotated non-coding RNA in a set of
                        genomic ranges
rnaCentralRetrieveEntry
                        Retrieves information for a specific entry of
                        the RNAcentral database
rnaCentralTextSearch    Searches the RNAcentral database with a text
                        query
writeCT                 Writes a file with the secondary structure of
                        an RNA in the CT format
writeDotBracket         Writes a file with the sequence and secondary
                        structure of an RNA in the Dot-Bracket format
