Tidyexposomics let’s you connect exposures, to phenotypes to omics, which is a lot of ground to cover! We provide a series of tutorials that take you through how to do this. We support exposure-phenotype only workflows and those with omics data included too.

Got an idea for a tutorial you want? Feel free to submit a request here!

0.0.1 Exposure-Phenotype Analysis

Data to have: exposures and phenotypes

0.0.2 Exposure-Phenotype-Omics Analysis

Data to have: exposures, omics, and phenotypes

Session Info 
sessionInfo()
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.5 LTS
## 
## Matrix products: default
## BLAS:   /home/biocbuild/bbs-3.24-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] tidyexposomics_1.1.3        MultiAssayExperiment_1.39.1
##  [3] SummarizedExperiment_1.43.0 Biobase_2.73.2             
##  [5] GenomicRanges_1.65.4        Seqinfo_1.3.2              
##  [7] IRanges_2.47.5              S4Vectors_0.51.10          
##  [9] BiocGenerics_0.59.12        generics_0.1.4             
## [11] MatrixGenerics_1.25.0       matrixStats_1.5.0          
## [13] BiocStyle_2.41.0           
## 
## loaded via a namespace (and not attached):
##   [1] splines_4.6.1         later_1.4.8           filelock_1.0.3       
##   [4] tibble_3.3.1          polyclip_1.10-7       rpart_4.1.27         
##   [7] factoextra_2.2.0      tidyHeatmap_1.13.1    lifecycle_1.0.5      
##  [10] httr2_1.3.0           Rdpack_2.6.6          rstatix_1.1.0        
##  [13] edgeR_4.99.12         doParallel_1.0.17     lattice_0.23-1       
##  [16] MASS_7.3-66           dendextend_1.19.1     backports_1.5.1      
##  [19] magrittr_2.0.5        limma_3.99.4          Hmisc_5.3-0          
##  [22] sass_0.4.10           rmarkdown_2.32        jquerylib_0.1.4      
##  [25] yaml_2.3.12           httpuv_1.6.17         otel_0.2.0           
##  [28] doRNG_1.8.6.3         DBI_1.3.0             RColorBrewer_1.1-3   
##  [31] abind_1.4-8           Rtsne_0.17            purrr_1.2.2          
##  [34] ggraph_2.2.2          itertools_0.1-3       nnet_7.3-21          
##  [37] tweenr_2.0.3          circlize_0.4.18       ggrepel_0.9.8        
##  [40] fenr_1.11.3           missForest_1.6.1      codetools_0.2-20     
##  [43] DelayedArray_0.39.8   DT_0.34.0             ggforce_0.5.0        
##  [46] shape_1.4.6.1         tidyselect_1.2.1      farver_2.1.2         
##  [49] viridis_0.6.5         dynamicTreeCut_1.63-1 BiocFileCache_3.3.1  
##  [52] base64enc_0.1-6       jsonlite_2.0.0        GetoptLong_1.1.1     
##  [55] tidygraph_1.3.1       Formula_1.2-6         ggridges_0.5.7       
##  [58] iterators_1.0.14      foreach_1.5.2         tools_4.6.1          
##  [61] Rcpp_1.1.2            glue_1.8.1            gridExtra_2.3.1      
##  [64] SparseArray_1.13.4    BiocBaseUtils_1.15.1  xfun_0.62            
##  [67] ranger_0.18.0         dplyr_1.2.1           withr_3.0.3          
##  [70] BiocManager_1.30.27   fastmap_1.2.0         ggh4x_0.3.1          
##  [73] digest_0.6.39         R6_2.6.1              mime_0.13            
##  [76] visdat_0.6.1          colorspace_2.1-4      Cairo_1.7-0          
##  [79] dichromat_2.0-1       RSQLite_3.53.3        utf8_1.2.6           
##  [82] tidyr_1.3.2           ggsci_5.2.0           data.table_1.18.6.1  
##  [85] FNN_1.1.4.1           graphlayouts_1.2.5    httr_1.4.9           
##  [88] htmlwidgets_1.6.4     S4Arrays_1.13.2       pkgconfig_2.0.3      
##  [91] gtable_0.3.6          blob_1.3.0            ComplexHeatmap_2.29.0
##  [94] S7_0.2.2              XVector_0.53.0        htmltools_0.5.9      
##  [97] carData_3.0-6         bookdown_0.48         naniar_1.1.0         
## [100] clue_0.3-68           scales_1.4.0          png_0.1-9            
## [103] knitr_1.52            rstudioapi_0.19.0     tzdb_0.5.0           
## [106] rjson_0.2.23          checkmate_2.3.4       curl_8.1.0           
## [109] cachem_1.1.0          GlobalOptions_0.1.4   stringr_1.6.0        
## [112] parallel_4.6.1        foreign_0.8-92        pillar_1.11.1        
## [115] grid_4.6.1            vctrs_0.7.3           promises_1.5.0       
## [118] randomForest_4.7-1.2  ggpubr_1.0.0          car_3.1-5            
## [121] dbplyr_2.6.0          xtable_1.8-8          cluster_2.1.8.3      
## [124] htmlTable_2.5.0       evaluate_1.0.5        readr_2.2.0          
## [127] tinytex_0.61          magick_2.9.1          cli_3.6.6            
## [130] compiler_4.6.1        rlang_1.3.0           crayon_1.5.3         
## [133] rngtools_1.5.2        ggsignif_0.6.4        labeling_0.4.3       
## [136] densityClust_0.3.3    tidybulk_2.3.3        forcats_1.0.1        
## [139] stringi_1.8.9         viridisLite_0.4.3     assertthat_0.2.1     
## [142] Matrix_1.7-6          hms_1.1.4             patchwork_1.3.2      
## [145] bit64_4.8.6           ggplot2_4.0.3         statmod_1.5.2        
## [148] shiny_1.14.0          rbibutils_2.4.1       igraph_2.3.4         
## [151] broom_1.0.13          memoise_2.0.1         bslib_0.12.0         
## [154] bit_4.6.0