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.
logoContext             Produces a motif of coding start context
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.
