DRomics

Dose Response for Omics


Licenses
CNRI-Python-GPL-Compatible/CNRI-Python-GPL-Compatible

Documentation

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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).

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

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