Welcome to the DRomicsInterpreter-shiny application
A second workflow for interpretation in light of a biological annotation



Links and resources

The DRomicsInterpreter-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 . You can find more information and help about the DRomicsInterpreter-shiny application and the DRomics package on this web page . Reading the vignette first and using the cheat sheet (both are available on this this page ) are recommended.

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/aursiber/DRomics/issues .


Citation and publications

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 ).


You can also look at the following citation for a complete example of use:

A multi-omics concentration-response framework uncovers novel understanding of triclosan effects in the chlorophyte Scenedesmus vacuolatus. Larras F, Billoir E, Scholz S, Tarkka M, Wubet T, Delignette-Muller ML, Schmitt-Jansen M (2020). Journal of Hazardous Materials. https://doi.org/10.1016/j.jhazmat.2020.122727




Import and merge of DRomics results and annotation data


Find here files for two examples (a file containing the DRomics results and another file containing biological annotations):
- an example about contigs: the Dromics output and the annotation data
- an example about metabolites: the DRomics output and the annotation data





Structure of the data frame merged and combined

              

First 3 lines of each experimental level in the data frame merged and combined



Trend and sensitivity plots


Selection of annotation groups to plot  














Structure of the data frame merged and combined


              




BMD plots (with and without gradient)








BMD plot with gradient






Curves plot





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


                


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