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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 normalize 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 sensitivity value (a benchmark dose or concentration) and a typology of response from each fitted curve.
In the available version data are supposed to be single-channel microarray data transformed in log2, or another type of data that can be directly fitted by least-square regression without any normalization step. In the future this tool will also be able to process RNA-seq data.


Sources & Documentation

DRomics is an R package, not yet but soon available on CRAN.

You can download the archive of the version 0.0-4 here above :

GZ - 1.1 Mo

Install the DRomics package on your computer with the following R command (where path_to_file is the path to the folder where you saved the archive) :
install.packages("path_to_file/dromics_0.0-4.tar.gz", repos = NULL, type="source")

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/


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

Coming soon ...