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 Gaussian distribution for each dose or concentration, with a common standard error. DRomics should not be used on other types of data.
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 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
Authors & Contacts
Elise Billoir - email@example.com - Laboratoire Interdisciplinaire des Environnements Continentaux - Université de Lorraine - Metz - France
Marie-Laure Delignette-Muller - firstname.lastname@example.org - Laboratoire de Biométrie et Biologie Evolutive - VetAgro Sup - Lyon - France
Floriane Larras - email@example.com - Department of Bioanalytical Ecotoxicology - Helmholtz Center for Environmental Research GmbH - Leipzig - Germany
Mechthild Schmitt-Jansen - firstname.lastname@example.org - Department of Bioanalytical Ecotoxicology - Helmholtz Center for Environmental Research GmbH - Leipzig - Germany
Aurélie Siberchicot - email@example.com - Laboratoire de Biométrie et Biologie Evolutive - Université Lyon 1 - Lyon - France
Issues can be reported on https://github.com/aursiber/DRomics/issues .
Grant Agreement number: 705149 - MicroERA - H2020-MSCA-IF-2015