Package: tima 2.11.0

Adriano Rutz

tima: Taxonomically Informed Metabolite Annotation

This package provides the infrastructure to perform Taxonomically Informed Metabolite Annotation.

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

tima_2.11.0.tar.gz
tima_2.11.0.zip(r-4.5)tima_2.11.0.zip(r-4.4)tima_2.11.0.zip(r-4.3)
tima_2.11.0.tgz(r-4.4-any)tima_2.11.0.tgz(r-4.3-any)
tima_2.11.0.tar.gz(r-4.5-noble)tima_2.11.0.tar.gz(r-4.4-noble)
tima_2.11.0.tgz(r-4.4-emscripten)tima_2.11.0.tgz(r-4.3-emscripten)
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'))

Peer review:

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

On CRAN:

metabolite annotationchemotaxonomyscoring systemnatural productscomputational metabolomicstaxonomic distancespecialized metabolome

37 exports 9 stars 3.11 score 126 dependencies 32 scripts

Last updated 24 days agofrom:bfaf53b9f7. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKAug 23 2024
R-4.5-winNOTEAug 23 2024
R-4.5-linuxNOTEAug 23 2024
R-4.4-winNOTEAug 23 2024
R-4.4-macNOTEAug 23 2024
R-4.3-winNOTEAug 23 2024
R-4.3-macNOTEAug 23 2024

Exports:annotate_massesannotate_spectracalculate_mass_of_mcreate_componentscreate_dircreate_edges_spectraexport_outputfilter_annotationsget_default_pathsget_example_filesget_fileget_last_version_from_zenodoget_organism_taxonomy_ottget_paramsgo_to_cacheimport_spectrainstalllog_debugparse_adductprepare_annotations_gnpsprepare_annotations_siriusprepare_annotations_spectraprepare_features_componentsprepare_features_edgesprepare_features_tablesprepare_libraries_rtprepare_libraries_sop_closedprepare_libraries_sop_ecmdbprepare_libraries_sop_hmdbprepare_libraries_sop_lotusprepare_libraries_sop_mergedprepare_libraries_spectraprepare_taxarun_appsanitize_spectratima_fullweight_annotations

Dependencies:anytimeapeaskpassbackportsbase64encbase64urlBHbigDBiocGenericsBiocParallelbitopsbslibcachemcallrcliclueclustercodetoolscolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledigestdocoptdplyrDTevaluatefansifarverfastmapfontawesomeformatRfsfstfstcorefutile.loggerfutile.optionsgenericsgluegthighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2igraphIRangesjquerylibjsonlitejuicyjuiceknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrmarkdownMASSMatrixmemoiseMetaboCoreUtilsmimeMsBackendMgfMsBackendMspMsCoreUtilsmsentropymunsellnlmeopensslpbapplypillarpkgconfigprettyunitsprocessxprogresspromisesProtGenericspsR6rappdirsRColorBrewerRcppreactablereactRrentrezrlangrmarkdownrnclrotlS4VectorssassscalessecretbaseshinyshinybusyshinyWidgetssnowsourcetoolsSpectrastringistringrsystargetstibbletidyfsttidyselecttidytabletinytexutf8V8vctrsviridisLitevisNetworkwithrxfunXMLxml2xtableyaml

General comments about the infrastructure

Adriano Rutz

Rendered fromtima.Rmdusingknitr::rmarkdownon Aug 23 2024.

Last update: 2024-08-16
Started: 2024-07-31

Readme and manuals

Help Manual

Help pageTopics
Annotate massesannotate_masses
Annotate spectraannotate_spectra
Benchmark taxize spectrabenchmark_taxize_spectra
Calculate entropycalculate_entropy
Calculate mass of Mcalculate_mass_of_m
Clean bioclean_bio
Clean chemoclean_chemo
Clean collapseclean_collapse
Columns modelcolumns_model
Complement metadata of structurescomplement_metadata_structures
Copy backbonecopy_backbone
Create componentscreate_components
Create directorycreate_dir
Create edgescreate_edges
Create edges spectracreate_edges_spectra
Decorate biodecorate_bio
Decorate chemodecorate_chemo
Decorate massesdecorate_masses
Distance between two elements in a distance matrixdist_get
Dist groupsdist_groups
Export outputexport_output
Export parametersexport_params
Export spectra RDSexport_spectra_rds
Extract spectra from a Spectra objectextract_spectra
Fake annotations columnsfake_annotations_columns
Fake ECMDBfake_ecmdb
Fake HMDBfake_hmdb
Fake LOTUSfake_lotus
Fake SOP columnsfake_sop_columns
Filter annotationsfilter_annotations
Filter high confidence only *[Experimental]*filter_high_confidence_only
Get default pathsget_default_paths
Get example filesget_example_files
Get example siriusget_example_sirius
Get fileget_file
Get GNPS Tablesget_gnps_tables
Get last version from Zenodoget_last_version_from_zenodo
Get MassBank spectraget_massbank_spectra
Get organism taxonomy (Open Tree of Life Taxonomy)get_organism_taxonomy_ott
Get parametersget_params
Go to cachego_to_cache
Harmonize adductsharmonize_adducts
Harmonize names siriusharmonize_names_sirius
Harmonize spectraharmonize_spectra
Import spectraimport_spectra
Installinstall
Load yaml filesload_yaml_files
Log debuglog_debug
Log pipelog_pipe
Parse adductparse_adduct
Parse CLI parametersparse_cli_params
Parse YAML parametersparse_yaml_params
Pre harmonize names siriuspre_harmonize_names_sirius
Prepare annotations GNPSprepare_annotations_gnps
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 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 paramsprepare_params
Prepare taxaprepare_taxa
Read from SIRIUS zipread_from_sirius_zip
Replace ID in file pathsreplace_id
Round realsround_reals
Run apprun_app
Sanitize spectrasanitize_spectra
Select annotations columnsselect_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 columnsselect_sop_columns
Split Structure Organism Pairs tablesplit_tables_sop
Tima Fulltima_full
Transform score sirius CSItransform_score_sirius_csi
Weight annotationsweight_annotations
Weight bioweight_bio
Weight chemoweight_chemo