filterHits              Filters framecalled data based on the mean
                        number of hits observed across a replicate
                        group.
findCDS                 Parses a transcriptome file looking for
                        start/stop codons in frame.
frameCounting           Counts aligned reads within coding sequence
                        regions by frame and footprint size, splitting
                        by frame and footprint size.
lengthDist              A function plotting the density of lengths in a
                        riboData object.
libScales               Generates library scaling factors from ribosome
                        footprint (and associated RNA) data.
plotCDS                 Plots average ribosome footprint alignment to
                        coding sequences at 5' and 3' ends.
plotTranscript          Plots ribosome footprint abundance and mRNA
                        coverage (if available) for a specific
                        transcript.
readRibodata            Reads ribosomal and (optionally) rna data from
                        alignment files.
readingFrame            Analyses frame called ribosome footprint data
                        within coding sequences and identifies likely
                        frame-shift of different length ribosome
                        footprint reads.
riboCoding-class        Class "riboCoding"
riboData-class          Class "riboData"
riboSeqR-package        Analysis of sequencing data from ribosome
                        profiling experiments.
rnaCounts               Extracts mRNA counts from a riboDat object for
                        a set of coding sequence coordinates.
sliceCounts             Slices out count data from riboCoding object
                        for use in differential translation analyses.
