A user-friendly integrative R package for quantifying and visualizing translation efficiency from sequencing data in diverse biological systems

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Documentation for package ‘tTEscanR’ version 0.99.2

• DESCRIPTION file
• User guides, package vignettes and other documentation
• Package NEWS
• Package README

Help Pages

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_metadata	Metadata of mRNA and tRNA data
default_tTEscanR_mRNA_data	mRNA Expression Data Subset
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
plotTargetComparison	Distribution Plot of Codon/Anticodon Usage or Amino Acid Demand/Supply Compared to a Target
plotTEscore	Violin Plot Displaying tTE Scores
runDEAnalysis	Perform Differential Expression Analysis Using DESeq2
runPipeline	Runs the Theoretical Translation Efficiency (tTE) Pipeline
showPoolContribution	Examine the Codon Pool Contribution
transformFormat	Transform the format of a table
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
updateObject	Update Assay in a tTEscanR object