Package: tima Title: Taxonomically Informed Metabolite Annotation Version: 2.13.0.9000 Authors@R: c( person(given = "Adriano", family = "Rutz", email = "adafede@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0443-9902")), person(given = "Pierre-Marie", family = "Allard", email = "pierre-marie.allard@unifr.ch", role = "ctb", comment = c(ORCID = "0000-0003-3389-2191")) ) Maintainer: Adriano Rutz Description: TIMA provides a reproducible workflow for taxonomically informed metabolite annotation from feature tables, MS/MS spectra, and optional external resources such as SIRIUS and GNPS outputs. It combines mass, spectral, taxonomic, and structural evidence into a transparent scoring framework that can be inspected step-by-step. The package targets metabolomics practitioners who need configurable, scriptable, and documented annotation pipelines for research and production settings. License: AGPL (>= 3) URL: https://github.com/taxonomicallyinformedannotation/tima, https://taxonomicallyinformedannotation.github.io/tima-shinylive, https://taxonomicallyinformedannotation.github.io/tima BugReports: https://github.com/taxonomicallyinformedannotation/tima/issues Depends: R (>= 4.4.0) Imports: archive (>= 1.1.13), BiocParallel (>= 1.44.0), cli (>= 3.6.6), docopt (>= 0.7.2), fs (>= 2.1.0), httr (>= 1.4.8), httr2 (>= 1.2.2), igraph (>= 2.3.1), jsonlite (>= 2.0.0), lgr (>= 0.5.2), lifecycle (>= 1.0.5), methods, MetaboCoreUtils (>= 1.18.1), MsBackendMgf (>= 1.18.0), MsBackendMsp (>= 1.14.0), MsCoreUtils (>= 1.22.1), msentropy (>= 0.1.4), purrr (>= 1.2.2), R.utils (>= 2.13.0), reticulate (>= 1.46.0), rlang (>= 1.2.0), rotl (>= 3.1.1), Spectra (>= 1.20.1), stats, stringi (>= 1.8.7), targets (>= 1.12.0), tidyselect (>= 1.2.1), tidytable (>= 0.11.2), utils, yaml (>= 2.3.12) Suggests: altdoc (>= 0.7.2), BiocManager (>= 1.30.27), BiocVersion (>= 3.22.0), grateful (>= 0.3.0), knitr (>= 1.51), pkgload (>= 1.5.2), quarto (>= 1.5.1), shiny (>= 1.13.0), shinyhelper (>= 0.3.2), shinyjs (>= 2.1.1), shinytest2 (>= 0.5.1), shinyvalidate (>= 0.1.3), spelling, testthat (>= 3.3.2), visNetwork (>= 2.1.4), withr (>= 3.0.2) SystemRequirements: python (>= 3.12, < 3.15) VignetteBuilder: quarto ByteCompile: TRUE Collate: 'logs_utils.R' 'errors_utils.R' 'validations_utils.R' 'safe_fread.R' 'add_xrefs_to_annotations.R' 'adduct_universe.R' 'adduct_universe_config.R' 'constants.R' 'adduct_universe_formula.R' 'adduct_universe_matching.R' 'adducts_utils.R' 'round_reals.R' 'mass_evidence.R' 'harmonize_adducts.R' 'parse_yaml_params.R' 'parse_cli_params.R' 'pkg_system_file.R' 'get_default_paths.R' 'get_path.R' 'get_params.R' 'dists_utils.R' 'decorate_masses.R' 'parse_adduct.R' 'calculate_mass_of_m.R' 'annotate_masses.R' 'annotate_masses_consistency.R' 'annotate_masses_coverage.R' 'annotate_masses_enforcement.R' 'annotate_masses_features.R' 'annotate_masses_hypothesis.R' 'columns_utils.R' 'annotate_spectra.R' 'assert_utils.R' 'benchmark_metrics_utils.R' 'benchmark_taxize_spectra.R' 'c_wrappers.R' 'sanitize_spectrum_matrix.R' 'calculate_similarity.R' 'calculate_entropy_and_similarity.R' 'load_yaml_files.R' 'go_to_cache.R' 'create_dir.R' 'change_params_small.R' 'clean_bio.R' 'summarize_results.R' 'filter_high_evidence_only.R' 'clean_chemo.R' 'clean_chemo_preprocessing.R' 'clean_chemo_candidates.R' 'complement_metadata_structures.R' 'copy_backbone.R' 'create_components.R' 'predicates_utils.R' 'create_edges.R' 'sanitize_spectra.R' 'read_mgf_opti.R' 'import_spectra.R' 'get_spectra_ids.R' 'create_edges_spectra.R' 'decorate_bio.R' 'decorate_chemo.R' 'evidence_validation_utils.R' 'export_output.R' 'export_params.R' 'export_spectra_rds.R' 'extract_spectra.R' 'fake_ecmdb.R' 'fake_hmdb.R' 'fake_lotus.R' 'fake_pubchemlite.R' 'filter_annotations.R' 'get_compounds_xrefs.R' 'retry_utils.R' 'get_file.R' 'get_example_sirius.R' 'get_example_files.R' 'get_gnps_tables.R' 'get_last_version_from_zenodo.R' 'get_organism_taxonomy_ott.R' 'globals.R' 'harmonize_names_sirius.R' 'harmonize_spectra.R' 'install.R' 'mass_evidence_hypothesis.R' 'mass_evidence_utils.R' 'move_file_safely.R' 'mztab_app_utils.R' 'mztab_schema_utils.R' 'mztab_parser.R' 'mztab_validate.R' 'pre_harmonize_names_sirius.R' 'process_smiles.R' 'select_annotations_columns.R' 'prepare_annotations_gnps.R' 'prepare_annotations_mzmine.R' 'read_mztab.R' 'prepare_annotations_mztab.R' 'select_sirius_columns.R' 'read_from_sirius_zip.R' 'prepare_annotations_sirius.R' 'prepare_annotations_sirius_utils.R' 'prepare_annotations_spectra.R' 'prepare_features_components.R' 'prepare_features_edges.R' 'rts_utils.R' 'prepare_features_tables.R' 'prepare_libraries_rt.R' 'select_sop_columns.R' 'prepare_libraries_sop_bigg.R' 'prepare_libraries_sop_closed.R' 'prepare_libraries_sop_ecmdb.R' 'prepare_libraries_sop_hmdb_like.R' 'prepare_libraries_sop_hmdb.R' 'prepare_libraries_sop_lotus.R' 'split_tables_sop.R' 'prepare_libraries_sop_merged.R' 'prepare_libraries_sop_merged_utils.R' 'prepare_libraries_sop_pubchemlite.R' 'prepare_libraries_spectra.R' 'prepare_params.R' 'prepare_taxa.R' 'replace_id.R' 'run_app.R' 'run_tima.R' 'sanitize_data.R' 'sanitize_data_utils.R' 'tima-package.R' 'transform_score_sirius_csi.R' 'validate_inputs.R' 'validations_params.R' 'weights_utils.R' 'weight_chemo.R' 'weight_bio.R' 'weight_annotations.R' 'weight_annotations_utils.R' 'write_mztab.R' 'write_mztab_comments.R' 'write_mztab_merge.R' 'write_mztab_metadata.R' 'write_mztab_tables.R' Config/roxygen2/markdown: TRUE Config/roxygen2/version: 8.0.0 Config/testthat/edition: 3 Encoding: UTF-8 Language: en-US biocViews: metaboliteAnnotation, chemotaxonomy, scoringSystem, naturalProducts, computationalMetabolomics, taxonomicDistance, specializedMetabolome X-schema.org-keywords: metaboliteAnnotation, chemotaxonomy, scoringSystem, naturalProducts, computationalMetabolomics, taxonomicDistance, specializedMetabolome Config/pak/sysreqs: cmake libglpk-dev make libarchive-dev libicu-dev libpng-dev libuv1-dev libxml2-dev libssl-dev python3 Repository: https://taxonomicallyinformedannotation.r-universe.dev Date/Publication: 2026-07-05 13:36:36 UTC RemoteUrl: https://github.com/taxonomicallyinformedannotation/tima RemoteRef: HEAD RemoteSha: d4283243a1b97e4e22d3c250756a5eea3ce12813 NeedsCompilation: yes Packaged: 2026-07-05 15:17:23 UTC; root Author: Adriano Rutz [aut, cre] (ORCID: ), Pierre-Marie Allard [ctb] (ORCID: )