Links and resources
The DRomicsInterpreter-shiny application runs on the shiny server of the LBBE with the develoment version of the DRomics package (available on Github ). DRomics is also an R package, available on CRAN . You can find more information and help about the DRomicsInterpreter-shiny application and the DRomics package on this web page . Reading the vignette first and using the cheat sheet (both are available on this this page ) are recommended.
If there seems to be a problem with the application, please send an explanatory e-mail at aurelie.siberchicot - at - univ-lyon1.fr.
Contact
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/lbbe-software/DRomics/issues .
Citation and publications
If you use Dromics Shiny App, you should cite:
DRomics, a workflow to exploit dose-response omics data in ecotoxicology. Delignette-Muller ML, Siberchicot A, Larras F, Billoir E (2023). Peer Community Journal. https://peercommunityjournal.org/articles/10.24072/pcjournal.325/
DRomics: a turnkey tool to support the use of the dose-response framework for omics data in ecological risk assessment. Larras F, Billoir E, Baillard V, Siberchicot A, Scholz S, Wubet T, Tarkka M, Schmitt-Jansen M and Delignette-Muller ML (2018). Environmental Science & Technology. https://doi.org/10.1021/acs.est.8b04752 (freely available at: https://hal.science/hal-02309919 ).
You can also look at the following citation for a complete example of use:
A multi-omics concentration-response framework uncovers novel understanding of triclosan effects in the chlorophyte Scenedesmus vacuolatus. Larras F, Billoir E, Scholz S, Tarkka M, Wubet T, Delignette-Muller ML, Schmitt-Jansen M (2020). Journal of Hazardous Materials. https://doi.org/10.1016/j.jhazmat.2020.122727
Import and merge of DRomics results and annotation data
- an example about contigs: the Dromics output and the annotation data
- an example about metabolites: the DRomics output and the annotation data
Trend and sensitivity plots
BMD plots (with and without gradient)
R CODE TO GO FURTHER
To see what more you can do using the R package, we recommend you to consult the vignette and the cheat sheet (links to all resources here ).
Download R Code
If there seems to be a problem with the application, please send an explanatory e-mail at aurelie.siberchicot - at - univ-lyon1.fr.