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.
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
To see what more you can do using the R package, we recommend you to consult the vignette and the cheat sheet of the package.