Man pages for taxonomicallyinformedannotation/tima-r
Taxonomically Informed Metabolite Annotation
| annotate_masses | Annotate masses |
| annotate_spectra | Annotate spectra |
| benchmark_taxize_spectra | Benchmark taxize spectra |
| calculate_entropy | Calculate entropy |
| calculate_mass_of_m | Calculate mass of M |
| change_params_small | Change Params Small |
| clean_bio | Clean bio |
| clean_chemo | Clean chemo |
| clean_collapse | Clean collapse |
| columns_model | Columns model |
| complement_metadata_structures | Complement metadata of structures |
| copy_backbone | Copy backbone |
| create_components | Create components |
| create_dir | Create directory |
| create_edges | Create edges |
| create_edges_spectra | Create edges spectra |
| decorate_bio | Decorate bio |
| decorate_chemo | Decorate chemo |
| decorate_masses | Decorate masses |
| dist_get | Distance between two elements in a distance matrix |
| dist_groups | Dist groups |
| export_output | Export output |
| export_params | Export parameters |
| export_spectra_rds | Export spectra RDS |
| extract_spectra | Extract spectra from a Spectra object |
| fake_annotations_columns | Fake annotations columns |
| fake_ecmdb | Fake ECMDB |
| fake_hmdb | Fake HMDB |
| fake_lotus | Fake LOTUS |
| fake_sop_columns | Fake SOP columns |
| filter_annotations | Filter annotations |
| filter_high_confidence_only | Filter high confidence only *[Experimental]* |
| get_default_paths | Get default paths |
| get_example_files | Get example files |
| get_example_sirius | Get example sirius |
| get_file | Get file |
| get_gnps_tables | Get GNPS Tables |
| get_last_version_from_zenodo | Get last version from Zenodo |
| get_massbank_spectra | Get MassBank spectra |
| get_organism_taxonomy_ott | Get organism taxonomy (Open Tree of Life Taxonomy) |
| get_params | Get parameters |
| go_to_cache | Go to cache |
| harmonize_adducts | Harmonize adducts |
| harmonize_names_sirius | Harmonize names sirius |
| harmonize_spectra | Harmonize spectra |
| import_spectra | Import spectra |
| install | Install |
| load_yaml_files | Load yaml files |
| log_debug | Log debug |
| log_pipe | Log pipe |
| parse_adduct | Parse adduct |
| parse_cli_params | Parse CLI parameters |
| parse_yaml_params | Parse YAML parameters |
| pre_harmonize_names_sirius | Pre harmonize names sirius |
| prepare_annotations_gnps | Prepare annotations GNPS |
| prepare_annotations_sirius | Prepare annotations SIRIUS |
| prepare_annotations_spectra | Prepare annotations MS2 |
| prepare_features_components | Prepare features components |
| prepare_features_edges | Prepare features edges |
| prepare_features_tables | Prepare features table |
| prepare_libraries_rt | Prepare libraries of retention times |
| prepare_libraries_sop_closed | Prepare libraries of structure organism pairs CLOSED |
| prepare_libraries_sop_ecmdb | Prepare libraries of structure organism pairs ECMDB |
| prepare_libraries_sop_hmdb | Prepare libraries of structure organism pairs HMDB |
| prepare_libraries_sop_lotus | Prepare libraries of structure organism pairs LOTUS |
| prepare_libraries_sop_merged | Prepare merged structure organism pairs libraries |
| prepare_libraries_spectra | Prepare libraries of spectra |
| prepare_params | Prepare params |
| prepare_taxa | Prepare taxa |
| read_from_sirius_zip | Read from SIRIUS zip |
| replace_id | Replace ID in file paths |
| round_reals | Round reals |
| run_app | Run app |
| sanitize_spectra | Sanitize spectra |
| select_annotations_columns | Select annotations columns |
| select_sirius_columns_canopus | Select sirius columns (canopus) |
| select_sirius_columns_formulas | Select sirius columns (formulas) |
| select_sirius_columns_structures | Select sirius columns (structures) |
| select_sop_columns | Select SOP columns |
| split_tables_sop | Split Structure Organism Pairs table |
| tima_full | Tima Full |
| tima-package | tima: Taxonomically Informed Metabolite Annotation |
| transform_score_sirius_csi | Transform score sirius CSI |
| weight_annotations | Weight annotations |
| weight_bio | Weight bio |
| weight_chemo | Weight chemo |
