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 normalize 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 and a typology of response from each fitted curve. In the available version data are supposed to be single-channel microarray data transformed in log2, or another type of data that can be directly fitted by least-square regression without any normalization step. In the future this tool will also be able to process RNA-seq data.

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

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


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




IMPORT, CHECK AND NORMALIZATION OF OMICS DATA


See here information about the format required
See here an example file (choose the 'cyclic loess' method to normalize these data)
See here information about the normalization methods

                  


SELECTION OF SIGNIFICANTLY RESPONSIVE ITEMS


See here information about the selection methods


                

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

                  



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