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DRomics

Overview

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, at least 6, and the more the better) 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).


All sources of DRomics are available at https://github.com/aursiber/DRomics.

The package

The limma and DESeq2 packages from Bioconductor must be installed for the use of DRomics :

if (!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install(c("limma", "DESeq2"))

The stable version of DRomics can be installed from CRAN using :
install.packages("DRomics")

The development version of DRomics can be installed from GitHub (remotes needed) :

if (!requireNamespace("remotes", quietly = TRUE))
  install.packages("remotes")
 
remotes::install_github("aursiber/DRomics")

Finally load the package in your current R session with the following R command :
library(DRomics)

The shiny app

DRomics-shiny can be run on a R session, doing :
shiny::runApp(system.file("DRomics-shiny", package = "DRomics"))

or online at :
http://lbbe-shiny.univ-lyon1.fr/DRomics-shiny/

This shiny app is runing with the development version of DRomics.


Authors & Contacts

Elise Billoir : elise.billoir@univ-lorraine.fr
Marie-Laure Delignette-Muller : marielaure.delignettemuller@vetagro-sup.fr
Floriane Larras : floriane.larras@ufz.de
Mechthild Schmitt-Jansen : mechthild.schmitt@ufz.de

About technical issues, you can contact Aurélie Siberchicot : aurelie.siberchicot@univ-lyon1.fr


Citation

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://pubs.acs.org/doi/10.1021/acs.est.8b04752