Welcome to the DRomics-shiny application
A first workflow for dose-response modelling


DRomics-shiny is a freely available tool for dose-response (or concentration-response) characterization from omics data. It is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of three replicates).
After a first optional step which consists to import, check and if needed normalize/transform the data (step 1), the aim of the proposed workflow is to select monotonic and/or biphasic significantly responsive items (e.g. probes, metabolites) (step 2), to choose the best-fit model among a predefined family of monotonic and biphasic models to describe the response of each selected item (step 3), and to derive a benchmark dose or concentration from each fitted curve (step 4).
In the available version, DRomics supports single-channel microarray data (in log2 scale), RNAseq data (in raw counts) or metabolomics data (in log scale). Proteomics data could also be handled as metabolomics data when expressed in intensity (continuous variable) or as RNAseq when expressed in spectral counts, after carefully checking the validity of the assumptions made in processing the RNAseq data. In order to link responses across biological levels based on a common method, DRomics also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. DRomics should not be used on other types of data.

Next, for interpretation of results in light of a biological annotation, you can use the DRomicsInterpreter-shiny application .

Links and resources

The DRomics-shiny application runs on the shiny server of the LBBE with the develoment version of the DRomics package (available on Github ). DRomics is also an R package, available on CRAN and on this web page , where you can find also a vignette and a cheat sheet.

If there seems to be a problem with the application, please send an explanatory e-mail at aurelie.siberchicot - at - univ-lyon1.fr.


Contact

If you have any need that is not yet covered, any feedback on the package / Shiny app, or any training needs, feel free to email us at dromics@univ-lyon1.fr . Issues can be reported on https://github.com/lbbe-software/DRomics/issues .


Citations

If you use Dromics Shiny App, you should cite:

DRomics, a workflow to exploit dose-response omics data in ecotoxicology. Delignette-Muller ML, Siberchicot A, Larras F, Billoir E (2023). Peer Community Journal. https://peercommunityjournal.org/articles/10.24072/pcjournal.325/

DRomics: a turnkey tool to support the use of the dose-response framework for omics data in ecological risk assessment. Larras F, Billoir E, Baillard V, Siberchicot A, Scholz S, Wubet T, Tarkka M, Schmitt-Jansen M and Delignette-Muller ML (2018). Environmental Science & Technology. https://doi.org/10.1021/acs.est.8b04752 (freely available at https://hal.science/hal-02309919 ).



IMPORT, CHECK AND PRETREATMENT OF OMICS DATA 



                

                
                

                

                  
                

                

              

            

          

          

            

              

                

                SELECTION OF SIGNIFICANTLY RESPONSIVE ITEMS
                

                

                

                

                  

                    
                  

                  

                    
                  

                

              

            

          

          

            

              

                

                DOSE RESPONSE MODELLING FOR RESPONSIVE ITEMS
                

                

                

                

                  

                    
                  

                  

                    

                    

                    

                    
                    

                    

                  

                

              

            

          

          

            

              

                

                COMPUTATION OF BENCHMARK DOSES FOR RESPONSIVE ITEMS
                

                

                

                

                  

                    
                  

                  

                    
                  

                

                

                

                

                  

                    
                  

                  

                    

                  

                

                

                

                

                  

                    
                  

                  

                    

                    

                    

                  

                

              

            

          

          

            

              

                

                R CODE TO GO FURTHER
                

                

                

                

                  To see what more you can do using the R package, we recommend you to consult the vignette and the cheat sheet
                  (links to all resources 
                  here
                  ).
                

                

                
                  
                  Download R Code
                
                

                

                

                

                

                
                  
                  Download R Code to go further
                
                

                

                

                

                

              

            

          

        

      

    
    

    If there seems to be a problem with the application, please send an explanatory e-mail at aurelie.siberchicot - at - univ-lyon1.fr.