This repository contains the code associated with the paper titled "Diet-omics in the Study of Urban and Rural Crohn Disease Evolution (SOURCE)".
This repository contains the code for conducting the multi-omic analysis performed in the study. It includes the scripts and resources necessary to reproduce the results and further analyze the data. For more detailed analysis and source data, please visit the SOURCE GitHub Repository.
To use the code in this repository, follow these steps:
- Clone the repository:
git clone https://github.com/Tzipisb/SOURCE.git- Install the required R packages specified in the session_info section.
- Get processed data from the paper and the second github repository SOURCE GitHub Repository.
- Set local path for data in SOURCE_analysis.Rmd
R version 4.0.2 (2020-06-22) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 22621)
Matrix products: default
locale: [1] LC_COLLATE=English_Israel.1252 LC_CTYPE=English_Israel.1252 LC_MONETARY=English_Israel.1252 LC_NUMERIC=C LC_TIME=English_Israel.1252
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] plotly_4.10.1 lubridate_1.8.0 forcats_1.0.0 readr_2.1.2 tidyverse_2.0.0 rstatix_0.7.2 vegan_2.6-2 permute_0.9-7
[9] ggdist_3.2.0 magrittr_2.0.3 stringr_1.4.0 yardstick_0.0.9 workflowsets_0.1.0 workflows_0.2.4 tune_0.1.6 tidyr_1.2.0
[17] tibble_3.1.6 rsample_1.1.0 recipes_0.2.0 purrr_0.3.4 parsnip_0.2.0 modeldata_1.1.0 infer_1.0.4 dplyr_1.0.8
[25] dials_0.1.0 scales_1.2.1 broom_1.0.3 tidymodels_0.1.4 mixOmics_6.14.1 ggplot2_3.3.5 lattice_0.20-45 MASS_7.3-56
loaded via a namespace (and not attached):
[1] readxl_1.4.0 backports_1.4.1 plyr_1.8.7 igraph_1.3.0 lazyeval_0.2.2 splines_4.0.2 BiocParallel_1.24.1
[8] listenv_0.9.0 digest_0.6.25 foreach_1.5.2 htmltools_0.5.2 fansi_1.0.3 cluster_2.1.3 tzdb_0.3.0
[15] globals_0.16.2 gower_1.0.0 matrixStats_0.62.0 rARPACK_0.11-0 vroom_1.5.7 hardhat_0.2.0 colorspace_2.0-3
[22] ggrepel_0.9.1 xfun_0.30 crayon_1.5.2 jsonlite_1.8.0 survival_3.3-1 iterators_1.0.14 glue_1.6.2
[29] gtable_0.3.1 ipred_0.9-12 distributional_0.3.2 car_3.1-1 future.apply_1.10.0 abind_1.4-5 DBI_1.1.3
[36] Rcpp_1.0.8.3 viridisLite_0.4.1 GPfit_1.0-8 bit_4.0.4 lava_1.7.2.1 prodlim_2019.11.13 htmlwidgets_1.5.4
[43] httr_1.4.5 RColorBrewer_1.1-3 ellipsis_0.3.2 pkgconfig_2.0.3 farver_2.1.0 nnet_7.3-17 utf8_1.2.2
[50] tidyselect_1.1.2 labeling_0.4.2 rlang_1.0.2 DiceDesign_1.9 reshape2_1.4.4 munsell_0.5.0 cellranger_1.1.0
[57] tools_4.0.2 cli_3.2.0 generics_0.1.3 evaluate_0.20 fastmap_1.1.0 yaml_2.3.5 knitr_1.37
[64] bit64_4.0.5 future_1.32.0 nlme_3.1-157 compiler_4.0.2 rstudioapi_0.14 lhs_1.1.5 stringi_1.7.6
[71] RSpectra_0.16-0 Matrix_1.4-1 vctrs_0.4.1 pillar_1.8.1 lifecycle_1.0.1 furrr_0.3.1 data.table_1.14.2
[78] corpcor_1.6.10 R6_2.5.1 gridExtra_2.3 parallelly_1.35.0 codetools_0.2-19 assertthat_0.2.1 withr_2.5.0
[85] mgcv_1.8-40 parallel_4.0.2 hms_1.1.3 grid_4.0.2 rpart_4.1.16 timeDate_4022.108 class_7.3-20
[92] rmarkdown_2.21 carData_3.0-5 pROC_1.18.0 ellipse_0.4.3