Section: Ecotoxicology & Environmental Chemistry
Topic:
Environmental sciences,
Genetics/Genomics
DRomics, a workflow to exploit dose-response omics data in ecotoxicology
Corresponding author(s): Delignette-Muller, Marie Laure (marielaure.delignettemuller@vetagro-sup.fr)
10.24072/pcjournal.325 - Peer Community Journal, Volume 3 (2023), article no. e90.
Get full text PDF Peer reviewed and recommended by PCIOmics 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 https://lbbe.univ-lyon1.fr/fr/dromics gathers links to all resources related to DRomics, including the two shiny applications.
Type: Outil logiciel
Delignette-Muller, Marie Laure 1; Siberchicot, Aurélie 1; Larras, Floriane 1; Billoir, Elise 2
@article{10_24072_pcjournal_325, author = {Delignette-Muller, Marie Laure and Siberchicot, Aur\'elie and Larras, Floriane and Billoir, Elise}, title = {DRomics, a workflow to exploit dose-response omics data in ecotoxicology}, journal = {Peer Community Journal}, eid = {e90}, publisher = {Peer Community In}, volume = {3}, year = {2023}, doi = {10.24072/pcjournal.325}, language = {en}, url = {https://peercommunityjournal.org/articles/10.24072/pcjournal.325/} }
TY - JOUR AU - Delignette-Muller, Marie Laure AU - Siberchicot, Aurélie AU - Larras, Floriane AU - Billoir, Elise TI - DRomics, a workflow to exploit dose-response omics data in ecotoxicology JO - Peer Community Journal PY - 2023 VL - 3 PB - Peer Community In UR - https://peercommunityjournal.org/articles/10.24072/pcjournal.325/ DO - 10.24072/pcjournal.325 LA - en ID - 10_24072_pcjournal_325 ER -
%0 Journal Article %A Delignette-Muller, Marie Laure %A Siberchicot, Aurélie %A Larras, Floriane %A Billoir, Elise %T DRomics, a workflow to exploit dose-response omics data in ecotoxicology %J Peer Community Journal %D 2023 %V 3 %I Peer Community In %U https://peercommunityjournal.org/articles/10.24072/pcjournal.325/ %R 10.24072/pcjournal.325 %G en %F 10_24072_pcjournal_325
Delignette-Muller, Marie Laure; Siberchicot, Aurélie; Larras, Floriane; Billoir, Elise. DRomics, a workflow to exploit dose-response omics data in ecotoxicology. Peer Community Journal, Volume 3 (2023), article no. e90. doi : 10.24072/pcjournal.325. https://peercommunityjournal.org/articles/10.24072/pcjournal.325/
PCI peer reviews and recommendation, and links to data, scripts, code and supplementary information: 10.24072/pci.ecotoxenvchem.100105
Conflict of interest of the recommender and peer reviewers:
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article.
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