Package: fobitools 1.15.1

Pol Castellano-Escuder

fobitools: Tools for Manipulating the FOBI Ontology

A set of tools for interacting with the Food-Biomarker Ontology (FOBI). A collection of basic manipulation tools for biological significance analysis, graphs, and text mining strategies for annotating nutritional data.

Authors:Pol Castellano-Escuder [aut, cre], Alex Sánchez-Pla [aut]

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fobitools.pdf |fobitools.html✨
fobitools/json (API)
NEWS

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

Bug tracker:https://github.com/pcastellanoescuder/fobitools/issues

Datasets:
  • fobi - FOBI Table File - Jul 23, 2021
  • fobi_terms - FOBI's 'ontology_index' object - Jul 23, 2021
  • foods - FOBI Foods Table File - Feb 02, 2021
  • idmap - FOBI Identifier Map File - Jul 18, 2021

On BioConductor:fobitools-1.15.1(bioc 3.21)fobitools-1.14.0(bioc 3.20)

massspectrometrymetabolomicssoftwarevisualizationbiomedicalinformaticsgraphandnetworkannotationcheminformaticspathwaysgenesetenrichmentbiological-intrerpretationbiological-knowledgebiological-significance-analysisenrichment-analysisfood-biomarker-ontologyknowledge-graphnutritionobofoundryontologytext-mining

5.30 score 1 stars 5 scripts 243 downloads 7 exports 118 dependencies

Last updated 3 months agofrom:fc658a64d2. Checks:1 OK, 7 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 27 2025
R-4.5-winNOTEJan 27 2025
R-4.5-macNOTEJan 27 2025
R-4.5-linuxNOTEJan 27 2025
R-4.4-winNOTEJan 27 2025
R-4.4-macNOTEJan 27 2025
R-4.3-winNOTEJan 27 2025
R-4.3-macNOTEJan 27 2025

Exports:%>%annotate_foodsfobi_graphid_convertmseaoraparse_fobi

Dependencies:adaBHBiocParallelbitbit64blobcachemclasscliclisymbolscodetoolscolorspacecowplotcpp11crayondata.tableDBIdiagramdigestdplyrdtte1071englishevdfansifarverfastmapfastmatchfffgseaformatRfutile.loggerfutile.optionsfuturefuture.applygenericsggforceggplot2ggraphggrepelglobalsgluegraphlayoutsgridExtragtablehmsigraphipredisobandjsonliteKernSmoothlabelinglambda.rlatticelavalexiconlifecyclelistenvmagrittrMASSMatrixmemoisemgcvmgsubmunsellnlmeNLPnnetnumDerivontologyIndexparallellypillarpkgconfigplogrpolyclipprettyunitsprodlimprogressprogressrproxypurrrqdapRegexR6RColorBrewerRcppRcppArmadilloRcppEigenRecordLinkagerlangrpartRSQLitescalesshapeslamsnowSQUAREMstringistringrsurvivalsystemfontssyuzhettextcleantextshapetibbletictoctidygraphtidyrtidyselecttweenrtzdbutf8vctrsviridisviridisLitevroomwithrxtablezoo

Dietary text annotation

Pol Castellano-Escuder

Rendered fromDietary_data_annotation.Rmdusingknitr::rmarkdownon Jan 27 2025.

Last update: 2022-01-12
Started: 2021-01-13

Simple food over representation analysis (ORA)

Pol Castellano-Escuder

Rendered fromfood_enrichment_analysis.Rmdusingknitr::rmarkdownon Jan 27 2025.

Last update: 2022-01-12
Started: 2021-01-13

Use case: LC-MS Based Approaches to Investigate Metabolomic Differences in the Urine of Young Women after Drinking Cranberry Juice or Apple Juice

Pol Castellano-Escuder

Rendered fromMW_ST000291_enrichment.Rmdusingknitr::rmarkdownon Jan 27 2025.

Last update: 2024-11-27
Started: 2021-05-08

Use case: Amino Acid Metabolites of Dietary Salt Effects on Blood Pressure in Human Urine

Pol Castellano-Escuder

Rendered fromMW_ST000629_enrichment.Rmdusingknitr::rmarkdownon Jan 27 2025.

Last update: 2024-11-27
Started: 2021-05-10