An R toolkit for non-coding RNA


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Documentation for package ‘ncRNAtools’ version 1.6.0

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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