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Postprocessing and univariate analysis of omics data

Bioconductor version: Release (3.19)

The 'phenomis' package provides methods to perform post-processing (i.e. quality control and normalization) as well as univariate statistical analysis of single and multi-omics data sets. These methods include quality control metrics, signal drift and batch effect correction, intensity transformation, univariate hypothesis testing, but also clustering (as well as annotation of metabolomics data). The data are handled in the standard Bioconductor formats (i.e. SummarizedExperiment and MultiAssayExperiment for single and multi-omics datasets, respectively; the alternative ExpressionSet and MultiDataSet formats are also supported for convenience). As a result, all methods can be readily chained as workflows. The pipeline can be further enriched by multivariate analysis and feature selection, by using the 'ropls' and 'biosigner' packages, which support the same formats. Data can be conveniently imported from and exported to text files. Although the methods were initially targeted to metabolomics data, most of the methods can be applied to other types of omics data (e.g., transcriptomics, proteomics).

Author: Etienne A. Thevenot [aut, cre] , Natacha Lenuzza [ctb], Marie Tremblay-Franco [ctb], Alyssa Imbert [ctb], Pierrick Roger [ctb], Eric Venot [ctb], Sylvain Dechaumet [ctb]

Maintainer: Etienne A. Thevenot <etienne.thevenot at>

Citation (from within R, enter citation("phenomis")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

phenomis-vignette HTML R Script
Reference Manual PDF


biocViews BatchEffect, Clustering, Coverage, KEGG, MassSpectrometry, Metabolomics, Normalization, Proteomics, QualityControl, Sequencing, Software, StatisticalMethod, Transcriptomics
Version 1.6.2
In Bioconductor since BioC 3.16 (R-4.2) (1.5 years)
License CeCILL
Depends SummarizedExperiment
Imports Biobase, biodb, biodbChebi, data.table, futile.logger, ggplot2, ggrepel, graphics, grDevices, grid, htmlwidgets, igraph, limma, methods, MultiAssayExperiment, MultiDataSet, PMCMRplus, plotly, ranger, RColorBrewer, ropls, stats, tibble, tidyr, utils, VennDiagram
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Suggests BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat
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Source Package phenomis_1.6.2.tar.gz
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macOS Binary (arm64) phenomis_1.6.2.tgz
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