Function reference
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annotate_masses() - Annotate masses
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annotate_spectra() - Annotate spectra
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calculate_entropy() - Calculate entropy
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clean_bio() - Clean bio
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clean_chemo() - Clean chemo
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clean_collapse() - Clean collapse
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cleanup_spectra() - Cleanup spectra
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columns_model() - A simplistic column model
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complement_metadata_structures() - Complement metadata of structures
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create_adducts() - Create adducts
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create_components() - Create components
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create_dir() - Create directory
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create_edges() - Create edges
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create_edges_spectra() - Create edges spectra
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decorate_bio() - Decorate bio
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decorate_chemo() - Decorate chemo
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decorate_masses() - Decorate masses
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dist_get() - Get the distance between two elements in a distance matrix
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dist_groups() - Dist groups
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export_output() - Export output
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export_params() - Export parameters
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export_spectra() - Export spectra
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export_spectra_2() - Export spectra 2
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extract_spectra() - Extract spectra from a Spectra object
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fake_annotations_columns() - Fake annotations columns
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fake_ecmdb() - Fake ECMDB
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fake_hmdb() - Fake HMDB
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fake_lotus() - Fake LOTUS
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fake_sop_columns() - Fake SOP columns
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filter_annotations() - Filter annotations
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filter_nitrogen_rule() - Filter nitrogen rule
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get_example_sirius() - Get example sirius
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get_file() - Get file
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get_gnps_tables() - Get GNPS Tables
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get_last_version_from_zenodo() - Get last version from Zenodo
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get_massbank_spectra() - Get MassBank spectra
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get_organism_taxonomy_ott() - Get organism taxonomy (Open Tree of Life Taxonomy)
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get_params() - Get parameters
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harmonize_names_sirius() - Harmonize names sirius
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harmonize_spectra() - Harmonize spectra
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import_spectra() - Import spectra
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install_latest_version() - Install latest version
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keep_peaks() - Keep peaks
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load_yaml_files() - Load yaml files
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log_debug() - Log debug
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log_pipe() - Log pipe
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normalize_peaks() - Normalize peaks
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parse_cli_params() - Parse CLI parameters
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parse_yaml_params() - Parse YAML parameters
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parse_yaml_paths() - Parse YAML paths
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pre_harmonize_names_sirius() - Pre harmonize names sirius
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prepare_annotations_gnps() - Prepare annotations GNPS
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prepare_annotations_sirius() - Prepare annotations SIRIUS
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prepare_annotations_spectra() - Prepare annotations MS2
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prepare_features_components() - Prepare features components
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prepare_features_edges() - Prepare features edges
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prepare_features_tables() - Prepare features table
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prepare_libraries_adducts() - Prepare libraries of adducts
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prepare_libraries_rt() - Prepare libraries of retention times
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prepare_libraries_sop_closed() - Prepare libraries of structure organism pairs CLOSED
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prepare_libraries_sop_ecmdb() - Prepare libraries of structure organism pairs ECMDB
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prepare_libraries_sop_hmdb() - Prepare libraries of structure organism pairs HMDB
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prepare_libraries_sop_lotus() - Prepare libraries of structure organism pairs LOTUS
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prepare_libraries_sop_merged() - Prepare merged structure organism pairs libraries
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prepare_libraries_spectra() - Prepare libraries of spectra
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prepare_params() - Prepare params
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prepare_taxa() - Prepare taxa
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read_from_sirius_zip() - Read from SIRIUS zip
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remove_above_precursor() - Remove peaks above precursor in MS2 spectra
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replace_id() - Replace ID in file paths
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round_reals() - Round reals
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sanitize_spectra() - Sanitize spectra
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select_annotations_columns() - Select annotations columns
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select_sirius_columns_canopus() - Select sirius columns (canopus)
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select_sirius_columns_formulas() - Select sirius columns (formulas)
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select_sirius_columns_structures() - Select sirius columns (structures)
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select_sop_columns() - Select SOP columns
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split_tables_sop() - Split Structure Organism Pairs table
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taxize_spectra_benchmark() - Taxize spectra benchmark
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weight_annotations() - Weight annotations
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weight_bio() - Weight bio
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weight_chemo() - Weight chemo