RiboProfiling           RiboProfiling.
aroundPromoter          Returns the flank size around the TSS for the x
                        % CDSs
cdsPosTransc            Per transcript relative position of start and
                        end codons for dataset ctrlGAlignments
codonDataCtrl           Codon frequency and coverage in ORFs on
                        chromosome 1, for dataset ctrlGAlignments
codonIndexCovCtrl       The read coverage for each codon in ORFs on
                        chromosome 1, for dataset ctrlGAlignments
codonInfo               Associates the read counts on codons with the
                        codon type for each ORF.
codonPCA                PCA graphs on codon coverage
countShiftReads         Apply an offset on the read start along the
                        transcript and returns the coverage on the
                        5pUTR, CDS, 3pUTR, as well as a matrix of codon
                        coverage per ORF.
countsPlot              Graphs of sample read counts (quality
                        assesment)
ctrlGAlignments         Ribosome profiling data on chr1 in human
                        primary BJ fibroblasts control data: PMID:
                        23594524.
histMatchLength         Histogram of match length distribution of
                        reads.
orfRelativePos          Relative position of the start and stop codon
                        along the transcript
plotSummarizedCov       Plots the summarized coverage in a specified
                        range (e.g. around TSS) for the specified match
                        sizes
printPCA                Plots the PCA scatterplots produced by codonPCA
                        function.
readStartCov            Read start coverage around the TSS on the
                        predifined CDSs
readsToStartOrEnd       Reads in GAlignments converted to either Read
                        Start (5') or End (3') Positions
riboSeqFromBAM          Starting from a BAM file path: quality plots,
                        shift ribosome position, coverage on multiple
                        transcript features and on codons.
