Package: tima 2.12.0.9000

Adriano Rutz

tima: Taxonomically Informed Metabolite Annotation

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.

Authors:Adriano Rutz [aut, cre], Pierre-Marie Allard [ctb]

tima_2.12.0.9000.tar.gz
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tima.pdf |tima.html✨
tima/json (API)
NEWS

# Install 'tima' in R:
install.packages('tima', repos = c('https://taxonomicallyinformedannotation.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/taxonomicallyinformedannotation/tima/issues

Pkgdown/docs site:https://taxonomicallyinformedannotation.github.io

On CRAN:

Conda:

metaboliteannotationchemotaxonomyscoringsystemnaturalproductscomputationalmetabolomicstaxonomicdistancespecializedmetabolomelc-msmsmetabolite-annotationmetabolomicsnatural-productsscoring-systemspecialized-metabolometaxonomyquarto

6.81 score 16 stars 2 packages 35 scripts 45 exports 89 dependencies

Last updated from:021c229b13. Checks:13 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-arm64OK197
linux-devel-x86_64OK218
source / vignettesOK257
linux-release-arm64OK221
linux-release-x86_64OK229
macos-release-arm64OK182
macos-release-x86_64OK384
macos-oldrel-arm64OK198
macos-oldrel-x86_64OK348
windows-develOK506
windows-releaseOK497
windows-oldrelOK484
wasm-releaseOK192

Exports:annotate_massesannotate_spectracalculate_mass_of_mcalculate_mz_from_masscalculate_similaritychange_params_smallcreate_componentscreate_edgescreate_edges_spectrafilter_annotationsget_compounds_xrefsget_example_filesget_fileget_gnps_tablesget_last_version_from_zenodoget_organism_taxonomy_ottgo_to_cacheharmonize_adductsimport_spectrainstallinstall_timaparse_adductprepare_annotations_gnpsprepare_annotations_mzmineprepare_annotations_siriusprepare_annotations_spectraprepare_features_componentsprepare_features_edgesprepare_features_tablesprepare_libraries_rtprepare_libraries_sop_biggprepare_libraries_sop_closedprepare_libraries_sop_ecmdbprepare_libraries_sop_hmdbprepare_libraries_sop_lotusprepare_libraries_sop_mergedprepare_libraries_spectraprepare_paramsprepare_taxaprocess_smilesrun_apprun_timatima_fullvalidate_inputsweight_annotations

Dependencies:apearchiveaskpassbackportsbase64urlBHBiocGenericsBiocParallelcallrcliclueclustercodetoolscpp11crayoncurldata.tabledigestdocoptdplyrevaluateformatRfsfutile.loggerfutile.optionsgenericsglueherehighrhmshttrhttr2igraphIRangesjsonliteknitrlambda.rlatticelgrlifecyclemagrittrMASSMatrixMetaboCoreUtilsmimeMsBackendMgfMsBackendMspMsCoreUtilsmsentropynlmeopensslpillarpkgconfigpngprettyunitsprocessxprogressProtGenericspspurrrR.methodsS3R.ooR.utilsR6rappdirsRcppRcppTOMLrentrezreticulaterlangrnclrotlrprojrootS4VectorssecretbasesnowSpectrastringisystargetstibbletidyselecttidytableutf8vctrswithrxfunXMLyaml

General comments about the infrastructure

Rendered fromtima.qmdusingquarto::htmlon Apr 21 2026.

Last update: 2026-04-15
Started: 2025-07-02

Readme and manuals

Help Manual

Help pageTopics
Annotate massesannotate_masses
Annotate spectraannotate_spectra
Calculate mass of Mcalculate_mass_of_m
Calculate m/z from neutral mass (inverse operation)calculate_mz_from_mass
Calculate similarity between spectracalculate_similarity
Change Parameters (Convenience Function)change_params_small
Clean Chemical Annotationsclean_chemo
Copy backbonecopy_backbone
Create componentscreate_components
Create spectral similarity network edgescreate_edges
Create edges spectracreate_edges_spectra
Filter annotationsfilter_annotations
Retrieve external database identifiers for compounds by InChIKey via Wikidataget_compounds_xrefs
Get example filesget_example_files
Get example siriusget_example_sirius
Download file from URLget_file
Get GNPS Tablesget_gnps_tables
Get Latest Version from Zenodoget_last_version_from_zenodo
Get organism taxonomy (Open Tree of Life Taxonomy)get_organism_taxonomy_ott
Navigate to cache directorygo_to_cache
Harmonize adduct notationsharmonize_adducts
Import spectraimport_spectra
Install TIMA Package and Dependencies (DEPRECATED)install
Install TIMA Package and Dependenciesinstall_tima
Parse adductparse_adduct
Prepare annotations GNPSprepare_annotations_gnps
Prepare annotations mzmineprepare_annotations_mzmine
Prepare annotations SIRIUSprepare_annotations_sirius
Prepare annotations MS2prepare_annotations_spectra
Prepare features componentsprepare_features_components
Prepare features edgesprepare_features_edges
Prepare features tableprepare_features_tables
Prepare libraries of retention timesprepare_libraries_rt
Prepare libraries of structure organism pairs BiGGprepare_libraries_sop_bigg
Prepare libraries of structure organism pairs CLOSEDprepare_libraries_sop_closed
Prepare libraries of structure organism pairs ECMDBprepare_libraries_sop_ecmdb
Prepare libraries of structure organism pairs HMDBprepare_libraries_sop_hmdb
Prepare libraries of structure organism pairs LOTUSprepare_libraries_sop_lotus
Prepare merged structure organism pairs librariesprepare_libraries_sop_merged
Prepare libraries of spectraprepare_libraries_spectra
Prepare workflow parametersprepare_params
Prepare taxaprepare_taxa
Process SMILES stringsprocess_smiles
Run TIMA Shiny apprun_app
Run Complete TIMA Workflowrun_tima
Run Complete TIMA Workflow (DEPRECATED)tima_full
Transform SIRIUS CSI scoretransform_score_sirius_csi
Validate Input Datavalidate_inputs
Weight annotationsweight_annotations