FLOSS                   Fragment Length Organization Similarity Score
                        (FLOSS)
PAmotif                 Metaplot of P site distribution
assignReadingFrame      Assign reading frame
codonUsage              Start or Stop codon usage
countReads              Extract counts for RPFs and RNAs
coverageDepth           Extract coverage depth for gene level or
                        transcript level
coverageRates           Calculate coverage rate
cvgd-class              Class '"cvgd"'
estimatePsite           Estimate P site position
filterCDS               Filter CDS by size
frameCounts             Extract counts for gene level or transcript
                        level
getFPKM                 Get FPKM values for counts
getORFscore             Calculate ORFscore
getPsiteCoordinates     Get P site coordinates
ggBar                   barplot by ggplot2
metaPlot                Metagene analysis plot
normByRUVs              Normalization by RUVSeq
plotDistance2Codon      Metaplot of P site distribution
plotFrameDensity        Plot density for each reading frame
plotSpliceEvent         Plot splice event
plotTE                  Plot translational efficiency
plotTranscript          Plot reads P site abundance for a specific
                        transcript
prepareCDS              Prepare CDS
readsDistribution       Plot reads distribution in genomic elements
readsEndPlot            Plot start/stop windows
readsLenToKeep          Get reads length to keep by cutoff percentage
ribosomeReleaseScore    Ribosome Release Score (RRS)
shiftReadsByFrame       Shift reads by reading frame
simulateRPF             Simulation function
spliceEvent             Get splicing events
strandPlot              Plot the distribution of reads in sense and
                        antisense strand
summaryReadsLength      Summary the reads lengths
translationalEfficiency
                        Translational Efficiency
