|generate_transcriptome||Generate transcriptome and genedf for alignment and analysis...|
|get_gene||Get coverage and ribosome occupancy of a gene by nucleotide|
|load_profiling_data||re-load pre-processed profiling data|
|metagene_bins||Divide ORF into bins and return either gene by gene or a...|
|metagene_cds||Get average ribosome footprint alignment values at the 5' and...|
|occupancy||Get ribosome occupancy at codon or amino acid level|
|phasing||Count the number of aligned reads per read length per frame|
|read_profiling_data||Read .bam files and pre-process them for further analysis|
|rrp||Calculate relative ribosome positioning|
|select_read_lengths||Select Relevant Read Lengths for the Profiling Library|
|smith||Ribosome profiling and RNA-Seq library from Smith et. al.|
|totals||Returns the total number of reads that map to an ORF and the...|
|write_profiling_data||Write profiling library list to file.|
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