Package: fobitools 1.15.0

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-1.15.0(bioc 3.21)fobitools-1.14.0(bioc 3.20)

massspectrometry metabolomics software visualization biomedicalinformatics graphandnetwork annotation cheminformatics pathways genesetenrichment biological-intrerpretation biological-knowledge biological-significance-analysis enrichment-analysis food-biomarker-ontology knowledge-graph nutrition obofoundry ontology text-mining

3.70 score 1 stars 5 scripts 187 downloads 7 exports 117 dependencies

Last updated 23 days agofrom:3dfb00eb35. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 19 2024
R-4.5-win	WARNING	Nov 19 2024
R-4.5-linux	WARNING	Nov 19 2024
R-4.4-win	WARNING	Nov 19 2024
R-4.4-mac	WARNING	Nov 19 2024
R-4.3-win	WARNING	Nov 19 2024
R-4.3-mac	WARNING	Nov 19 2024

Exports:%>%annotate_foods fobi_graph id_convert msea ora parse_fobi

Dependencies:ada BH BiocParallel bit bit64 blob cachem class cli clisymbols codetools colorspace cowplot cpp11 crayon data.table DBI diagram digest dplyr dtt e1071 english evd fansi farver fastmap fastmatch ff fgsea formatR futile.logger futile.options future future.apply generics ggforce ggplot2 ggraph ggrepel globals glue graphlayouts gridExtra gtable hms igraph ipred isoband KernSmooth labeling lambda.r lattice lava lexicon lifecycle listenv magrittr MASS Matrix memoise mgcv mgsub munsell nlme NLP nnet numDeriv ontologyIndex parallelly pillar pkgconfig plogr polyclip prettyunits prodlim progress progressr proxy purrr qdapRegex R6 RColorBrewer Rcpp RcppArmadillo RcppEigen RecordLinkage rlang rpart RSQLite scales shape slam snow SQUAREM stringi stringr survival systemfonts syuzhet textclean textshape tibble tictoc tidygraph tidyr tidyselect tweenr tzdb utf8 vctrs viridis viridisLite vroom withr xtable zoo

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Text Mining Pipeline to Annotate Free Nutritional Text with FOBI	annotate_foods
FOBI Table File - Jul 23, 2021	fobi
Generate FOBI Graphs	fobi_graph
FOBI's `ontology_index` object - Jul 23, 2021	fobi_terms
FOBI Foods Table File - Feb 02, 2021	foods
Convert Metabolite Identifiers	id_convert
FOBI Identifier Map File - Jul 18, 2021	idmap
Performs a preranked metabolite set enrichment analysis (MSEA)	msea
Classical Over Representation Analysis with FOBI	ora
Parse FOBI in a Readable Tabular Format	parse_fobi