Man pages for amandamok/choros
Bias Correction for Ribosome Profiling Data
| calculate_codon_density | Calculate codon density |
| calculate_transcript_density | Calculate per-transcript RPF density |
| choose_subsets | Choose RPF lengths and frames to model |
| choros | Pipeline for RPF bias correction |
| compute_rpf_gc | Compute GC-content for a ribosome-protected fragment |
| convert_to_aa | Convert from DNA to amino acid sequence |
| correct_bias | Correct for sequence biases in RPF counts |
| count_d5_d3 | Count RPFs by 5' and 3' digest lengths |
| count_footprints | Count RPFs by position, frame, and length |
| count_nonzero_codons | Count nonzero codon positions per transcript |
| evaluate_bias | Evaluate positional contributions to RPF counts |
| get_bias_seq | Retrieve nucleotides at RPF ends |
| get_codons | Retrieve codons in A-, P-, and E-site positions |
| init_data | Generate data frame to fit negative binomial regression model |
| load_anno | Load a transcriptome lengths file |
| load_bam | Pre-process RPF alignment file |
| match_rows | Get indices for corresponding rows in two data frames |
| parse_coefs | Annotate regression coefficients |
| plot_bias | Plot RPF biases |
| plot_coefs | Visualize regression coefficients |
| plot_diagnostic | Generate diagnostic plots |
| write_fasta | Write transcriptome sequence to disk |
