bamtobed                From BAM files to BED files.
bamtolist               From BAM files to lists of data tables or
                        GRangesList objects.
bedtolist               From BED files to lists of data tables or
                        GRangesList objects.
cds_coverage            Number of in-frame P-sites per coding sequence.
codon_coverage          Number of reads per codon.
codon_usage_psite       Empirical codon usage indexes.
create_annotation       Annotation data table.
duplicates_filter       Duplicates filtering.
frame_psite             Percentage of P-sites per reading frame.
frame_psite_length      Percentage of P-sites per reading frame
                        stratified by read length.
length_filter           Read length filtering.
metaheatmap_psite       Ribosome occupancy metaheatmaps at
                        single-nucleotide resolution.
metaprofile_psite       Ribosome occupancy metaprofiles at
                        single-nucleotide resolution.
mm81cdna                Annotation data table
psite                   Ribosome P-sites position within reads.
psite_info              Update reads information according to the
                        inferred P-sites.
psite_offset            P-site offsets data table
reads_list              Reads information data table
region_psite            Percentage of P-sites per transcript region.
rends_heat              Metaheatmaps of the two extremities of the
                        reads.
rlength_distr           Read length distributions.
