fobitools
This is the released version of fobitools; for the devel version, see fobitools.
Tools for Manipulating the FOBI Ontology
Bioconductor version: Release (3.23)
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.
Author: Pol Castellano-Escuder [aut, cre]
, Alex Sánchez-Pla [aut]
Maintainer: Pol Castellano-Escuder <polcaes at gmail.com>
citation("fobitools")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("fobitools")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("fobitools")| Dietary text annotation | HTML | R Script |
| Simple food ORA | HTML | R Script |
| Use case ST000291 | HTML | R Script |
| Use case ST000629 | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Annotation, BiomedicalInformatics, Cheminformatics, GeneSetEnrichment, GraphAndNetwork, MassSpectrometry, Metabolomics, Pathways, Software, Visualization |
| Version | 1.20.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (5 years) |
| License | GPL-3 |
| Depends | R (>= 4.1) |
| Imports | clisymbols, crayon, dplyr, fgsea, ggplot2, ggraph, magrittr, ontologyIndex, purrr, RecordLinkage, stringr, textclean, tictoc, tidygraph, tidyr, vroom |
| System Requirements | |
| URL | https://github.com/pcastellanoescuder/fobitools/ |
| Bug Reports | https://github.com/pcastellanoescuder/fobitools/issues |
See More
| Suggests | BiocStyle, covr, ggrepel, kableExtra, knitr, metabolomicsWorkbenchR, POMA, rmarkdown, rvest, SummarizedExperiment, testthat (>= 2.3.2), tidyverse |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fobitools_1.20.0.tar.gz |
| Windows Binary (x86_64) | fobitools_1.20.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | fobitools_1.20.0.tgz |
| macOS Binary (sonoma-arm64) | fobitools_1.20.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/fobitools |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fobitools |
| Bioc Package Browser | https://code.bioconductor.org/browse/fobitools/ |
| Package Short Url | https://bioconductor.org/packages/fobitools/ |
| Package Downloads Report | Download Stats |