Simple food over representation analysis (ORA) (original) (raw)
Contents
- 1 Installation
- 2 Load fobitools
- 3 metaboliteUniverse and metaboliteList
- 4 Network visualization of metaboliteList terms
- 5 Session Information
- References
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)
#>
#> 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
#> [7] BiocGenerics_0.54.0 generics_0.1.3
#> [9] MatrixGenerics_1.20.0 matrixStats_1.5.0
#> [11] metabolomicsWorkbenchR_1.18.0 POMA_1.18.0
#> [13] ggrepel_0.9.6 rvest_1.0.4
#> [15] kableExtra_1.4.0 lubridate_1.9.4
#> [17] forcats_1.0.0 stringr_1.5.1
#> [19] dplyr_1.1.4 purrr_1.0.4
#> [21] readr_2.1.5 tidyr_1.3.1
#> [23] tibble_3.2.1 ggplot2_3.5.2
#> [25] tidyverse_2.0.0 fobitools_1.16.0
#> [27] BiocStyle_2.36.0
#>
#> loaded via a namespace (and not attached):
#> [1] rstudioapi_0.17.1 jsonlite_2.0.0
#> [3] MultiAssayExperiment_1.34.0 magrittr_2.0.3
#> [5] magick_2.8.6 farver_2.1.2
#> [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
#> [15] qdapRegex_0.7.10 tictoc_1.2.1
#> [17] SparseArray_1.8.0 sass_0.4.10
#> [19] parallelly_1.43.0 bslib_0.9.0
#> [21] impute_1.82.0 RecordLinkage_0.4-12.4
#> [23] cachem_1.1.0 igraph_2.1.4
#> [25] lifecycle_1.0.4 pkgconfig_2.0.3
#> [27] Matrix_1.7-3 R6_2.6.1
#> [29] fastmap_1.2.0 GenomeInfoDbData_1.2.14
#> [31] future_1.40.0 selectr_0.4-2
#> [33] digest_0.6.37 syuzhet_1.0.7
#> [35] colorspace_2.1-1 ps_1.9.1
#> [37] RSQLite_2.3.9 labeling_0.4.3
#> [39] timechange_0.3.0 abind_1.4-8
#> [41] httr_1.4.7 polyclip_1.10-7
#> [43] compiler_4.5.0 proxy_0.4-27
#> [45] bit64_4.6.0-1 withr_3.0.2
#> [47] BiocParallel_1.42.0 viridis_0.6.5
#> [49] DBI_1.2.3 ggforce_0.4.2
#> [51] MASS_7.3-65 lava_1.8.1
#> [53] DelayedArray_0.34.0 textclean_0.9.3
#> [55] tools_4.5.0 chromote_0.5.0
#> [57] future.apply_1.11.3 nnet_7.3-20
#> [59] glue_1.8.0 promises_1.3.2
#> [61] grid_4.5.0 fgsea_1.34.0
#> [63] gtable_0.3.6 lexicon_1.2.1
#> [65] tzdb_0.5.0 class_7.3-23
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#> [69] hms_1.1.3 XVector_0.48.0
#> [71] tidygraph_1.3.1 xml2_1.3.8
#> [73] pillar_1.10.2 limma_3.64.0
#> [75] vroom_1.6.5 later_1.4.2
#> [77] splines_4.5.0 tweenr_2.0.3
#> [79] lattice_0.22-7 survival_3.8-3
#> [81] bit_4.6.0 tidyselect_1.2.1
#> [83] knitr_1.50 gridExtra_2.3
#> [85] bookdown_0.43 svglite_2.1.3
#> [87] xfun_0.52 graphlayouts_1.2.2
#> [89] statmod_1.5.0 stringi_1.8.7
#> [91] UCSC.utils_1.4.0 yaml_2.3.10
#> [93] evaluate_1.0.3 codetools_0.2-20
#> [95] evd_2.3-7.1 ggraph_2.2.1
#> [97] BiocManager_1.30.25 cli_3.6.4
#> [99] ontologyIndex_2.12 rpart_4.1.24
#> [101] xtable_1.8-4 systemfonts_1.2.2
#> [103] struct_1.20.0 munsell_0.5.1
#> [105] processx_3.8.6 jquerylib_0.1.4
#> [107] Rcpp_1.0.14 globals_0.16.3
#> [109] parallel_4.5.0 blob_1.2.4
#> [111] ff_4.5.2 listenv_0.9.1
#> [113] viridisLite_0.4.2 ipred_0.9-15
#> [115] scales_1.3.0 prodlim_2024.06.25
#> [117] e1071_1.7-16 crayon_1.5.3
#> [119] clisymbols_1.2.0 rlang_1.1.6
#> [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.