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README.md
# fobitools <img src='man/figures/logo.png' align="right" height="139" /> <!-- badges: start --> [![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://www.tidyverse.org/lifecycle/#stable) [![Build Status](https://travis-ci.com/pcastellanoescuder/fobitools.svg?branch=master)](https://travis-ci.com/pcastellanoescuder/fobitools) [![AppVeyor build status](https://ci.appveyor.com/api/projects/status/github/pcastellanoescuder/fobitools?branch=master&svg=true)](https://ci.appveyor.com/project/pcastellanoescuder/fobitools) [![Actions Status](https://github.com/pcastellanoescuder/fobitools/workflows/R-CMD-check/badge.svg)](https://github.com/pcastellanoescuder/fobitools/actions) [![Codecov test coverage](https://codecov.io/gh/pcastellanoescuder/fobitools/branch/master/graph/badge.svg)](https://codecov.io/gh/pcastellanoescuder/fobitools?branch=master) [![CodeFactor](https://www.codefactor.io/repository/github/pcastellanoescuder/fobitools/badge)](https://www.codefactor.io/repository/github/pcastellanoescuder/fobitools) [![Last Commit](https://img.shields.io/github/last-commit/pcastellanoescuder/fobitools.svg)](https://github.com/pcastellanoescuder/fobitools/commits/master) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0) [![DOI](https://img.shields.io/badge/DOI-https%3A%2F%2Fdoi.org%2F10.1093%2Fdataba%2Fbaaa033-blue)](https://doi.org/10.1093/databa/baaa033) <!-- badges: end --> This package provides a collection of tools to interact with [FOBI (Food-Biomarker Ontology)](https://github.com/pcastellanoescuder/FoodBiomarkerOntology). Some functionalities are: - Graph visualization of FOBI - Parse the last version of FOBI into a readable table format - Compound ID conversion (among metabolite names, FOBI, ChemSpider, KEGG, PubChemCID, InChIKey, InChICode, and HMDB) - Biological significance analysis via a classical over representation analysis - **Chemical class enrichment analysis**: Over representation analysis using FOBI chemical classes as sets - **Food group enrichment analysis**: Over representation analysis using FOBI food groups as sets `fobitools` also offers a Shiny app version called FOBI Visualization Tool. This application implements most of `fobitools` functions in an user-friendly web interface and it’s available at <http://webapps.nutrimetabolomics.com/FOBI_Visualization_Tool>. # Installation To install GitHub devel version use: ``` r # install.packages("devtools") devtools::install_github("pcastellanoescuder/fobitools") ``` ## Citation **Pol Castellano-Escuder, Raúl González-Domínguez, David S Wishart, Cristina Andrés-Lacueva, Alex Sánchez-Pla**, *FOBI: an ontology to represent food intake data and associate it with metabolomic data*, Database, Volume 2020, 2020, baaa033. DOI: <https://doi.org/10.1093/databa/baaa033> # Code of Conduct Please note that the ‘fobitools’ project is released with a [Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this project, you agree to abide by its terms.