Man pages for taxonomicallyinformedannotation/tima-r
Taxonomically Informed Metabolite Annotation
| annotate_masses | Annotate masses |
| annotate_spectra | Annotate spectra |
| calculate_entropy | Calculate entropy |
| clean_bio | Clean bio |
| clean_chemo | Clean chemo |
| clean_collapse | Clean collapse |
| columns_model | A simplistic column model |
| complement_metadata_structures | Complement metadata of structures |
| create_adducts | Create adducts |
| 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 | Get the distance between two elements in a distance matrix |
| dist_groups | Dist groups |
| export_output | Export output |
| export_params | Export parameters |
| export_spectra | Export spectra |
| export_spectra_2 | Export spectra 2 |
| 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_nitrogen_rule | Filter nitrogen rule |
| 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 |
| harmonize_names_sirius | Harmonize names sirius |
| harmonize_spectra | Harmonize spectra |
| import_spectra | Import spectra |
| install_latest_version | Install latest version |
| keep_peaks | Keep peaks |
| load_yaml_files | Load yaml files |
| log_debug | Log debug |
| log_pipe | Log pipe |
| normalize_peaks | Normalize peaks |
| parse_cli_params | Parse CLI parameters |
| parse_yaml_params | Parse YAML parameters |
| parse_yaml_paths | Parse YAML paths |
| 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_adducts | Prepare libraries of adducts |
| 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 |
| remove_above_precursor | Remove peaks above precursor in MS2 spectra |
| replace_id | Replace ID in file paths |
| round_reals | Round reals |
| sanitize_spectra | Sanitize spectra |
| select_annotations_columns | Select annotations columns |
| select_sirius_columns | Select sirius columns |
| select_sirius_columns_2 | Select sirius columns 2 |
| select_sop_columns | Select SOP columns |
| split_tables_sop | Split Structure Organism Pairs table |
| taxize_spectra_benchmark | Taxize spectra benchmark |
| weight_annotations | Weight annotations |
| weight_bio | Weight bio |
| weight_chemo | Weight chemo |
