An R toolkit for non-coding RNA

Documentation for package ‘ncRNAtools’ version 1.2.1

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