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.
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 - firstname.lastname@example.org - Laboratoire Interdisciplinaire des Environnements Continentaux - Université de Lorraine - Metz - France
Marie-Laure Delignette-Muller - email@example.com - Laboratoire de Biométrie et Biologie Evolutive - VetAgro Sup - Lyon - France
Floriane Larras - firstname.lastname@example.org - Department of Bioanalytical Ecotoxicology - Helmholtz Center for Environmental Research GmbH - Leipzig - Germany
Mechthild Schmitt-Jansen - email@example.com - Department of Bioanalytical Ecotoxicology - Helmholtz Center for Environmental Research GmbH - Leipzig - Germany
Aurélie Siberchicot - firstname.lastname@example.org - Laboratoire de Biométrie et Biologie Evolutive - Université Lyon 1 - Lyon - France
Grant Agreement number: 705149 - MicroERA - H2020-MSCA-IF-2015