Package index • tima

All functions

annotate_masses(): Annotate masses

annotate_spectra(): Annotate spectra

benchmark_taxize_spectra(): Benchmark taxize spectra

calculate_entropy_score(): Calculate entropy score

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

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

transform_score_sirius_csi(): Transform score sirius CSI

weight_annotations(): Weight annotations

weight_bio(): Weight bio

weight_chemo(): Weight chemo