computeAAUsage          Compute Amino Acid (AA) Demand or Supply
computeAnticodonUsage   Compute Anticodon Usage from tRNA Gene
                        Expression Data
computeCodonUsage       Compute Codon Usage from mRNA Gene Expression
                        Data
computeCorrelationBackground
                        Compute the Correlation Between Mean Usage and
                        Exonic Background
computeDEResults        Compute the DESeq2 Analysis
computeExonicBackground
                        Compute the Exonic Background of the
                        Codon/Anticodon Usage
computeMeanUsage        Compute Usage Across Conditions (Mean Usage)
computeTheoreticalTE    Compute the Theoretical Translation Efficiency
                        (tTE) score
controlVerbose          Control tTEscanR message output
createObject            Create a tTEscanR object as a
                        MultiAssayExperiment
default_tTEscanR_mRNA_data
                        mRNA Expression Data Subset
default_tTEscanR_metadata
                        Metadata of mRNA and tRNA data
default_tTEscanR_tRNA_data
                        tRNA Expression Data Subset
extractCodons           Extract Codon Composition of Sequences
featuresToAA            Relates Codons, Anticodons and their
                        corresponding Amino Acids
getCodonFreq            Compute Codon Frequency-per-Gene Table
getPermutationDist      Run Codon Usage Permutation Test (Background)
groupConditions         Aggregates data by group
mergeMatrices           Combine large matrices
obtainSignificance      Assess Significance (P-value) & Corrects for
                        Multiple Hypothesis Testing
plotCorrelation         Correlation Plot: Exonic Codon Background -
                        Mean Codon Usage
plotDEResults           Generates Visualizations from the DEA data
plotDistribution        Distribution Plot of Codon/Anticodon Usage or
                        Amino Acid Demand/Supply
plotPermutation         Permutation Plot
plotProportion          Proportion Plot of Codon/Anticodon Usage or
                        Amino Acid Demand/Supply
plotTEscore             Violin Plot Displaying tTE Scores
plotTargetComparison    Distribution Plot of Codon/Anticodon Usage or
                        Amino Acid Demand/Supply Compared to a Target
runDEAnalysis           Perform Differential Expression Analysis Using
                        DESeq2
runPipeline             Runs the Theoretical Translation Efficiency
                        (tTE) Pipeline
showPoolContribution    Examine the Codon Pool Contribution
tRNAFilterCuts          Filter Out Conditions With Low tRNA Cuts
tRNAGetMatrix           Generate a tRNA expression matrix
tRNASetCutoff           Selection of the Optimal tRNA Cut Cutoff
tRNASetGenes            Annotate the tRNA genes from tRNA tags
transformFormat         Transform the format of a table
updateObject            Update Assay in a tTEscanR object
