DRomics, a workflow to exploit dose-response omics data in ecotoxicology use asterix (*) to get italics

Marie Laure Delignette-Muller, Aurélie Siberchicot, Floriane Larras, Elise BilloirPlease use the format "First name initials family name" as in "Marie S. Curie, Niels H. D. Bohr, Albert Einstein, John R. R. Tolkien, Donna T. Strickland"

2023

<p style="text-align: justify;">Omics technologies has opened new possibilities to assess environmental risks and to understand the mode(s) of action of pollutants. Coupled to dose-response experimental designs, they allow a non-targeted assessment of organism responses at the molecular level along an exposure gradient. However, describing the dose-response relationships on such high-throughput data is no easy task. In a first part, we review the software available for this purpose, and their main features. We set out arguments on some statistical and modeling choices we have made while developing the R package DRomics and its positioning compared to others tools. The DRomics main analysis workflow is made available through a web interface, namely a shiny app named DRomics-shiny. Next, we present the new functionalities recently implemented. DRomics has been augmented especially to be able to handle varied omics data considering the nature of the measured signal (e.g. counts of reads in RNAseq) and the way data were collected (e.g. batch effect, situation with no experimental replicates). Another important upgrade is the development of tools to ease the biological interpretation of results. Various functions are proposed to visualize, summarize and compare the responses, for different biological groups (defined from biological annotation), optionally at different experimental levels (e.g. measurements at several omics level or in different experimental conditions). A new shiny app named DRomicsInterpreter-shiny is dedicated to the biological interpretation of results. The institutional web page <a href="https://lbbe.univ-lyon1.fr/fr/dromics" target="_blank" rel="noopener">https://lbbe.univ-lyon1.fr/fr/dromics</a> gathers links to all resources related to DRomics, including the two shiny applications.</p>

https://cran.r-project.org/web/packages/DRomics/vignettes/DRomics_vignette.htmlYou should fill this box only if you chose 'Scripts were used to obtain or analyze the results'. URL must start with http:// or https://

https://cran.r-project.org/web/packages/DRomics/index.htmlYou should fill this box only if you chose 'Codes have been used in this study'. URL must start with http:// or https://

Dose-response modeling, BenchMark Dose (BMD), Adverse Outcome Pathway (AOP), Mode of Action (MoA), environmental risk assessment, toxicogenomics, transcriptomics, proteomics, metabolomics, multi-omics

NonePlease indicate the methods that may require specialised expertise during the peer review process (use a comma to separate various required expertises).

Aquatic ecotoxicology, Environmental risk assessment, Genetics / Genomics, Marine ecotoxicology, Microbial ecotoxicology, Modelling, Terrestrial ecotoxicology

Jinhee Choi (jinhchoi@uos.ac.kr), Nicolas Creusot (nicolas.creusot@inrae.fr), Benjamin Marie (benjamin.marie@mnhn.fr), M.F. Vokuev (vokuevmihail11@gmail.com), Rebecca Beauvais (rebecca.beauvais@centreecotox.ch), Béatrice Gagnaire (beatrice.gagnaire@irsn.fr) No need for them to be recommenders of PCI Ecotox Env Chem. Please do not suggest reviewers for whom there might be a conflict of interest. Reviewers are not allowed to review preprints written by close colleagues (with whom they have published in the last four years, with whom they have received joint funding in the last four years, or with whom they are currently writing a manuscript, or submitting a grant proposal), or by family members, friends, or anyone for whom bias might affect the nature of the review - see the code of conduct

2023-02-17 15:39:03

Claudia Cosio

Rebecca Beauvais