aggregateCodPot         Aggregate Coding Potential Tool Results
annotateInteractions    Annotate Genomic Interactions with Functional
                        Enrichment Results
bestTool                Evaluate Performance of Coding Potential Tools
bestToolAtleast         Evaluate Performance of Agreement Thresholds
bestToolCombination     Evaluate Performance of Tool Combinations
calculateCM             Calculate and Filter Confusion Matrices for
                        Tool Combinations
createTrainTestSets     Split a Set of Sequence Names into Training and
                        Test Sets
evaluateToolCombinations
                        Evaluate Performance of Tool Combinations
evaluateToolsThresholds
                        Evaluate Agreement Thresholds Among Coding
                        Potential Tools
findCisInteractions     Find Potential cis-Regulatory Interactions from
                        FEELnc Output
findTransInteractions   Estimates trans-interactions between lncRNAs
                        and target RNAs based on expression
                        correlation. This function requires the 'Hmisc'
                        and 'tidyr' packages.
getBiotypes             Extract Gene or Transcript Biotypes from a
                        GRanges Object
getGtfStats             Extract Transcript Statistics from a GTF object
plotClockMetrics        Create Clock Plots for Confusion Matrix Metrics
plotRadarMetrics        Create Radar Plots for Confusion Matrix Metrics
plotSankeyInteractions
                        Plot Functional Interactions as a Sankey
                        Diagram
plotVennCodPot          Create Venn Diagram from Coding Potential
                        Results
prepareEvaluationSets   Prepare Data Sets for Performance Evaluation
