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| calc_cutoffs_from_profiles | Calculate offsets from 5'end profiles |
| choose_readlengths | Filter read lengths for P-sites position calculation |
| create_html_report | Create the Ribo-seQC analysis report in html |
| create_pdfs_from_rds_objects | Generate PDF files from RDS object files |
| FaFile_Circ | A simple extension to the FaFile class that allows one to include a list of circular ranges, e.g. chrM |
| FaFile_Circ-class | A simple extension to the FaFile class that allows one to include a list of circular ranges, e.g. chrM |
| getSeq-method | Yields the sequence for a particular range on a circular Fasta File note that |
| get_codon_usage_data | Get codon usage data (positional and bulk) |
| get_default_rl_selection | Get default choice of read lengths |
| get_metagene_data | Get 5'/P-site profile data for metagene analysis |
| get_ps_fromsplicemin | Offset spliced reads on minus strand |
| get_ps_fromspliceplus | Offset spliced reads on plus strand |
| get_rl_and_cutoffs | Get selected read lengths and cutoffs |
| get_top50_all_genes | Get top 50 abundant genes (all genes) |
| get_top50_cds_genes | Get top 50 abundant genes (CDS regions for protein coding genes) |
| get_top50_mapping | Get top 50 mapping positions |
| load_annotation | Load genomic features and genome sequence |
| plot_codon_usage_bulk | Plot bulk codon usage bar plots |
| plot_codon_usage_bulk_rmd | Plot bulk codon usage bar plots within the RMarkdown document |
| plot_codon_usage_positional | Plot positional codon usage heatmap |
| plot_codon_usage_positional_rmd | Plot positional codon usage heatmaps within the RMarkdown document |
| plot_frame_dist_boxplot | Plot frame coverage of 5'-site profiles |
| plot_frame_dist_boxplot_rmd | Plot frame coverage of 5'-site profiles within the RMarkdown document |
| plot_metagene_bar | Plot 5'/P-site profile per read length as barplot |
| plot_metagene_bar_rmd | Plot 5'/P-site profile per read length as barplot in R Markdown |
| plot_metagene_hm | Plot 5'/P-site profiles (for all read lengths) as heatmap |
| plot_metagene_hm_rmd | Plot 5'/P-site profiles as heatmaps within the RMarkdown document |
| plot_read_biotype_dist_1 | Plot read location distribution by biotype (and originating compartment) |
| plot_read_biotype_dist_2 | Plot read location distribution by originating compartment (and biotype) |
| plot_read_biotype_dist_by_length | Plot read length and location distribution (distribution per read length) |
| plot_read_length_dist | Plot read length distribution |
| plot_read_length_dist_by_biotype | Plot read length and location distribution (distribution per biotype) |
| prepare_annotation_files | Prepare comprehensive sets of annotated genomic features |
| RiboseQC_analysis | Perform a Ribo-seQC analysis |
| seqinfo-method | Yields a seqinfo object for the FaFile_Circ with it's circular ranges slot set appropriately |