Man pages for bartongroup/RATS
Relative Abundance of Transcripts
| alloc_out | Create output structure. |
| annot2ids | (deprecated) Extract matching transcript and gene IDs from a... |
| annot2models | Prepare GTF for gene model plotting. |
| annotation_inconsistent | Feature IDs match between |
| calculate_DTU | Set up and execute the tests. |
| call_DTU | Calculate differential transcript usage. |
| denest_sleuth_boots | Extract bootstrap counts into a less nested structure. |
| do_boot | Perform the bootstraps. |
| dtu_plurality_summary | Summary of DTU plurality. |
| dtu_summary | Summary of DTU calling. |
| dtu_switch_summary | Summary of isoform switching events. |
| fish4rodents | Import abundances directly from kallisto output. |
| get_dtu_ids | List of DTU ids. |
| get_plurality_ids | List the gene IDs by number of isoforms showing significant... |
| get_switch_ids | List of genes that switch isoform ranks. |
| granges2ids | Extract matching transcript and gene IDs from a GRanges... |
| group_samples | Group samples by covariate value. |
| g.test.1 | Log-likelihood test of goodness of fit. |
| g.test.2 | Log-likelihood test of independence. |
| gtf2ids | Extract matching transcript and gene IDs from a GTF file. |
| infer_bootnum | Rule-of-thumb number of iterations. |
| maxabs | Get largest value by absolute comparison. |
| parameters_are_good | Check input parameters. |
| plot_diagnostics | Plot diagnostics. |
| plot_gene | Plot abundances for all isoforms of a specified gene. |
| plot_overview | Plot DTU results overview. |
| plot_shiny_volcano | Interactive volcano plot, using shiny. |
| scale_data | Apply scaling. |
| sim_boot_data | Generate an artificial dataset of bootstrapped abundance... |
| sim_count_data | Generate an artificial dataset of abundance estimates, for... |
| structure_data | Structure input data. |
| tidy_annot | Tidy up annotation. |
