Package: DRomics 2.6-0

Aurelie Siberchicot

DRomics: Dose Response for Omics

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>.

Authors:Marie-Laure Delignette-Muller [aut], Elise Billoir [aut], Floriane Larras [ctb], Aurelie Siberchicot [aut, cre]

DRomics_2.6-0.tar.gz
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DRomics.pdf |DRomics.html✨
DRomics/json (API)
NEWS

# Install 'DRomics' in R:
install.packages('DRomics', repos = c('https://lbbe-software.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/lbbe-software/dromics/issues

Datasets:
  • Scenedesmus_apical - Concentration-response effect of triclosan in Scenedesmus vacuolatus
  • Scenedesmus_metab - Concentration-response effect of triclosan in Scenedesmus vacuolatus
  • Zhou_kidney_pce - Dose-response kidney transcriptomic effect of Tetrachloroethylene in mouse
  • zebraf - Transcriptomic dose-response to ionizing radiation in zebrafish with batch effect

On CRAN:

23 exports 5 stars 2.51 score 77 dependencies 33 scripts 377 downloads

Last updated 4 days agofrom:3a4f32b45a. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winOKSep 12 2024
R-4.5-linuxOKSep 12 2024
R-4.4-winOKSep 12 2024
R-4.4-macOKSep 12 2024
R-4.3-winOKSep 12 2024
R-4.3-macOKSep 12 2024

Exports:bmdbootbmdcalcbmdfilterbmdplotbmdplotwithgradientcontinuousanchoringdatacontinuousomicdatacurvesplotdrcfitecdfplotwithCIecdfquantileplotformatdata4DRomicsitemselectmetabolomicdatamicroarraydataomicdataPCAdataplotplotfit2pdfRNAseqdataselectgroupssensitivityplottargetplottrendplot

Dependencies:abindaskpassBHBiobaseBiocGenericsBiocParallelclicodetoolscolorspacecpp11crayoncurlDelayedArrayDESeq2dplyrfansifarverformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggfortifyggplot2gluegridExtragtablehttrIRangesisobandjsonlitelabelinglambda.rlatticelifecyclelimmalocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmeopensslpillarpkgconfigpurrrR6RColorBrewerRcppRcppArmadillorlangS4ArraysS4VectorsscalessnowSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc

Overview of the DRomics package

Marie Laure Delignette-Muller, Aurélie Siberchicot, Elise Billoir, Floriane Larras

Rendered fromDRomics_vignette.Rmdusingknitr::rmarkdownon Sep 12 2024.

Last update: 2024-08-02
Started: 2020-12-22

Readme and manuals

Help Manual

Help pageTopics
Computation of confidence interval on benchmark doses by bootstrapbmdboot plot.bmdboot print.bmdboot
Computation of benchmark doses for responsive itemsbmdcalc plot.bmdcalc print.bmdcalc
Filtering BMDs according to estimation qualitybmdfilter
BMD plot optionally with confidence intervals on BMDbmdplot
BMD plot with color gradientbmdplotwithgradient
Import and check of continuous anchoring apical datacontinuousanchoringdata plot.continuousanchoringdata print.continuousanchoringdata
Import and check of continuous omic data (e.g. metabolomic data)continuousomicdata metabolomicdata plot.continuousomicdata print.continuousomicdata
Plot of fitted curvescurvesplot
Dose response modelling for responsive itemsdrcfit plot.drcfit plotfit2pdf print.drcfit
ECDF plot of a variable with given confidence intervals on this variableecdfplotwithCI
ECDF plot of a given quantile of a variable calculated by groupecdfquantileplot
Build an R object that can be used as data input in DRomicsformatdata4DRomics
Selection of significantly responsive itemsitemselect print.itemselect
Import, check and normalization of single-channel microarray datamicroarraydata omicdata plot.microarraydata print.microarraydata
Performs and plots the results of a PCA on omic dataPCAdataplot
Import, check and normalization and transformation of RNAseq dataplot.RNAseqdata print.RNAseqdata RNAseqdata
Concentration-response effect of triclosan in Scenedesmus vacuolatusScenedesmus Scenedesmus_apical Scenedesmus_metab
Selection of groups on which to focusselectgroups
Plot of a summary of BMD values per group of itemssensitivityplot
Dose-reponse plot for target itemstargetplot
Plot of the repartition of trends per grouptrendplot
Transcriptomic dose-response to ionizing radiation in zebrafish with batch effectzebraf
Dose-response kidney transcriptomic effect of Tetrachloroethylene in mouseZhou Zhou_kidney_pce