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, at least 6, and the more the better) 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).

DRomics Shiny App runs on the shiny server of the LBBE (see here the DRomics tutorial ).

DRomics is also an R package, available on CRAN and on this web page .


If you use Dromics Shiny App, you can 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


Authors & Contacts

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@ufz.de - Department of Bioanalytical Ecotoxicology - Helmholtz Center for Environmental Research GmbH - Leipzig - Germany

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


Technical maintainer

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 NORMALIZATION OF OMICS DATA




See here information about the format required
See here an example file
See here information about the normalization methods
See here information about the format required
See here an example file
See here information about the transformation methods
See here information about the format required
See here an example file
We recommend you to check that your metabolomics data were correctly pretreated before importation. In particular data (metabolomic signal) should have been log-transformed, without replacing 0 values by NA values (consider using the half minimum method instead for example).
See here more information about metabolomics data pretreatment

                  
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SELECTION OF SIGNIFICANTLY RESPONSIVE ITEMS


See here information about the selection methods

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DOSE RESPONSE MODELLING FOR RESPONSIVE ITEMS


Click this button each time you update a setting in previous steps:
See here information about the dose reponse modelling procedure
These ongoing calculations can take from minutes to about an hour. Your patience should be proportional to the size of your data and the chosen FDR.

                  
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COMPUTATION OF BENCHMARK DOSES FOR RESPONSIVE ITEMS


See here information about the BMD-zSD and the BMD-xfold

Download results
See here information about the provided results

                





See here information about typologies

Download figure