Welcome to the DRomics Shiny Application


DRomics is a freely available on-line 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). 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.

DRomics Shiny App 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 DRomics Shiny App 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


Grant Agreement number: 705149 - MicroERA - H2020-MSCA-IF-2015

Horizon 2020




IMPORT, CHECK AND PRETREATMENT OF OMICS DATA



              
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SELECTION OF SIGNIFICANTLY RESPONSIVE ITEMS


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DOSE RESPONSE MODELLING FOR RESPONSIVE ITEMS



                  

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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 here the vignette of the package.

Download R Code


              

Download R Code to go further