Simple food over representation analysis (ORA) (original) (raw)

Contents

Compiled date: 2025-04-15

Last edited: 2022-01-12

License: GPL-3

Installation

Run the following code to install the Bioconductor version of the package.

# install.packages("BiocManager")
BiocManager::install("fobitools")

Session Information

sessionInfo()
#> R version 4.5.0 RC (2025-04-04 r88126)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.2 LTS
#> 
#> Matrix products: default
#> BLAS:   /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so 
#> LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_GB              LC_COLLATE=C              
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: America/New_York
#> tzcode source: system (glibc)
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#> attached base packages:
#> [1] stats4    stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] SummarizedExperiment_1.38.0   Biobase_2.68.0               
#>  [3] GenomicRanges_1.60.0          GenomeInfoDb_1.44.0          
#>  [5] IRanges_2.42.0                S4Vectors_0.46.0             
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#> [11] metabolomicsWorkbenchR_1.18.0 POMA_1.18.0                  
#> [13] ggrepel_0.9.6                 rvest_1.0.4                  
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#> [17] forcats_1.0.0                 stringr_1.5.1                
#> [19] dplyr_1.1.4                   purrr_1.0.4                  
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#> [23] tibble_3.2.1                  ggplot2_3.5.2                
#> [25] tidyverse_2.0.0               fobitools_1.16.0             
#> [27] BiocStyle_2.36.0             
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#> loaded via a namespace (and not attached):
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#>   [3] MultiAssayExperiment_1.34.0 magrittr_2.0.3             
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#>   [7] rmarkdown_2.29              vctrs_0.6.5                
#>   [9] memoise_2.0.1               tinytex_0.57               
#>  [11] BiocBaseUtils_1.10.0        S4Arrays_1.8.0             
#>  [13] htmltools_0.5.8.1           curl_6.2.2                 
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#>  [17] SparseArray_1.8.0           sass_0.4.10                
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#>  [97] BiocManager_1.30.25         cli_3.6.4                  
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#> [121] ada_2.0-5                   cowplot_1.1.3              
#> [123] fastmatch_1.1-6

References

Castellano-Escuder, Pol, Raúl González-Domı́nguez, David S Wishart, Cristina Andrés-Lacueva, and Alex Sánchez-Pla. 2020. “FOBI: An Ontology to Represent Food Intake Data and Associate It with Metabolomic Data.” Database 2020.