# Dose Response for Omics

## Documentation for package ‘DRomics’ version 2.6-2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

bmdboot | Computation of confidence interval on benchmark doses by bootstrap
bmdcalc | Computation of benchmark doses for responsive items
bmdfilter | Filtering BMDs according to estimation quality
bmdplot | BMD plot optionally with confidence intervals on BMD
bmdplotwithgradient | BMD plot with color gradient
continuousanchoringdata | Import and check of continuous anchoring apical data
continuousomicdata | Import and check of continuous omic data (e.g. metabolomic data)
curvesplot | Plot of fitted curves
drcfit | Dose response modelling for responsive items
ecdfplotwithCI | ECDF plot of a variable with given confidence intervals on this variable
ecdfquantileplot | ECDF plot of a given quantile of a variable calculated by group
formatdata4DRomics | Build an R object that can be used as data input in DRomics
itemselect | Selection of significantly responsive items
metabolomicdata | Import and check of continuous omic data (e.g. metabolomic data)
microarraydata | Import, check and normalization of single-channel microarray data
omicdata | Import, check and normalization of single-channel microarray data
PCAdataplot | Performs and plots the results of a PCA on omic data
plot.bmdboot | Computation of confidence interval on benchmark doses by bootstrap
plot.bmdcalc | Computation of benchmark doses for responsive items
plot.continuousanchoringdata | Import and check of continuous anchoring apical data
plot.continuousomicdata | Import and check of continuous omic data (e.g. metabolomic data)
plot.drcfit | Dose response modelling for responsive items
plot.microarraydata | Import, check and normalization of single-channel microarray data
plot.RNAseqdata | Import, check and normalization and transformation of RNAseq data
plotfit2pdf | Dose response modelling for responsive items
print.bmdboot | Computation of confidence interval on benchmark doses by bootstrap
print.bmdcalc | Computation of benchmark doses for responsive items
print.continuousanchoringdata | Import and check of continuous anchoring apical data
print.continuousomicdata | Import and check of continuous omic data (e.g. metabolomic data)
print.drcfit | Dose response modelling for responsive items
print.itemselect | Selection of significantly responsive items
print.microarraydata | Import, check and normalization of single-channel microarray data
print.RNAseqdata | Import, check and normalization and transformation of RNAseq data
RNAseqdata | Import, check and normalization and transformation of RNAseq data
Scenedesmus | Concentration-response effect of triclosan in Scenedesmus vacuolatus
Scenedesmus_apical | Concentration-response effect of triclosan in Scenedesmus vacuolatus
Scenedesmus_metab | Concentration-response effect of triclosan in Scenedesmus vacuolatus
selectgroups | Selection of groups on which to focus
sensitivityplot | Plot of a summary of BMD values per group of items
targetplot | Dose-reponse plot for target items
trendplot | Plot of the repartition of trends per group
zebraf | Transcriptomic dose-response to ionizing radiation in zebrafish with batch effect
Zhou | Dose-response kidney transcriptomic effect of Tetrachloroethylene in mouse
Zhou_kidney_pce | Dose-response kidney transcriptomic effect of Tetrachloroethylene in mouse