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phenomis

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 cea.fr>

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

Installation

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


if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("phenomis")

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

Documentation

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

browseVignettes("phenomis")
phenomis-vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews BatchEffect, Clustering, Coverage, KEGG, MassSpectrometry, Metabolomics, Normalization, Proteomics, QualityControl, Sequencing, Software, StatisticalMethod, Transcriptomics
Version 1.6.0
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
System Requirements
URL https://doi.org/10.1038/s41597-021-01095-3
See More
Suggests BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package phenomis_1.6.0.tar.gz
Windows Binary phenomis_1.6.0.zip (64-bit only)
macOS Binary (x86_64) phenomis_1.6.0.tgz
macOS Binary (arm64) phenomis_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/phenomis
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/phenomis
Bioc Package Browser https://code.bioconductor.org/browse/phenomis/
Package Short Url https://bioconductor.org/packages/phenomis/
Package Downloads Report Download Stats