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


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 and on this web page .

You can find help about the DRomicsInterpreter-shiny application and the DRomics package in a vignette and a cheat sheet .


Citation and publications

If you use Dromics Shiny App, you should cite:

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


You can freely find this article at: https://hal.archives-ouvertes.fr/hal-02309919


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

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


Contacts and authors

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 .


Elise Billoir - elise.billoir@univ-lorraine.fr - Laboratoire Interdisciplinaire des Environnements Continentaux - Université de Lorraine - Metz - France

Marie-Laure Delignette-Muller - marielaure.delignettemuller@vetagro-sup.fr - Laboratoire de Biométrie et Biologie Evolutive - VetAgro Sup - Lyon - France

Floriane Larras - floriane.larras@inrae.fr - Delegation for scientific expertise, foresight and advanced studies (DEPE) - INRAE - Paris - France

Mechthild Schmitt-Jansen - mechthild.schmitt@ufz.de - Department of Bioanalytical Ecotoxicology - Helmholtz Center for Environmental Research GmbH - Leipzig - Germany

Aurélie Siberchicot - aurelie.siberchicot@univ-lyon1.fr - Laboratoire de Biométrie et Biologie Evolutive - Université Lyon 1 - Lyon - France


Import and merge of DRomics results and 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

            
              
              Download Data
            
          





BMD plots (with and without 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 of the package.

Download R Code