# RiboseQC, a Comprehensive Ribo-Seq Analysis Tool

## Documentation for package ‘RiboseQC’ version 1.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

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