Optimization of ribosome P-site positioning in ribosome profiling data

Documentation for package ‘riboWaltz’ version 1.2.0

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.