CRAN/E | DRomics

DRomics

Dose Response for Omics

Installation

About

Several functions are provided for dose-response (or concentration-response) characterization from omics data. 'DRomics' is especially dedicated to omics data obtained using a typical dose-response design, favoring a great number of tested doses (or concentrations) rather than a great number of replicates (no need of replicates). 'DRomics' provides functions 1) to check, normalize and or transform data, 2) to select monotonic or biphasic significantly responding items (e.g. probes, metabolites), 3) to choose the best-fit model among a predefined family of monotonic and biphasic models to describe each selected item, 4) to derive 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 in log2, RNAseq data in raw counts, or already pretreated continuous omics data (such as metabolomic data) in log scale. In order to link responses across biological levels based on a common method, 'DRomics' also handles apical data as long as they are continuous and follow a normal distribution for each dose or concentration, with a common standard error. For further details see Delignette-Muller et al (2023) doi:10.24072/pcjournal.325 and Larras et al (2018) doi:10.1021/acs.est.8b04752.

Citation DRomics citation info
lbbe.univ-lyon1.fr/fr/dromics
aursiber.github.io/DRomics/
Bug report File report

Key Metrics

Version 2.5-2
R ≥ 3.5.0
Published 2024-01-31 75 days ago
Needs compilation? no
License GPL-2
License GPL-3
CRAN checks DRomics results

Downloads

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Maintainer

Maintainer

Aurelie Siberchicot

aurelie.siberchicot@univ-lyon1.fr

Authors

Marie-Laure Delignette-Muller

aut

Elise Billoir

aut

Floriane Larras

ctb

Aurelie Siberchicot

aut / cre

Contacts

Marie-Laure Delignette-Muller

Material

NEWS
Reference manual
Package source

In Views

Omics

Vignettes

Overview of the DRomics package

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

DRomics archive

Depends

R ≥ 3.5.0
limma
utils
grDevices
DESeq2
SummarizedExperiment

Imports

stats
graphics
ggplot2
ggfortify
rlang

Suggests

parallel
shiny
shinyBS
shinycssloaders
shinyjs
shinyWidgets
sortable
testthat
knitr
rmarkdown
sva
VennDiagram
plotly
svglite