phenomis

DOI: 10.18129/B9.bioc.phenomis  

This package is for version 3.17 of Bioconductor; for the stable, up-to-date release version, see phenomis.

Postprocessing and univariate analysis of omics data

Bioconductor version: 3.17

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>

Installation

To install this package, start R (version "4.3") 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")

 

HTML	R Script	phenomis-vignette
PDF		Reference Manual
Text		NEWS

Details

biocViews	BatchEffect, Clustering, Coverage, KEGG, MassSpectrometry, Metabolomics, Normalization, Proteomics, QualityControl, Sequencing, Software, StatisticalMethod, Transcriptomics
Version	1.2.0
In Bioconductor since	BioC 3.16 (R-4.2) (1 year)
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
LinkingTo
Suggests	BiocGenerics, BiocStyle, biosigner, CLL, knitr, omicade4, rmarkdown, testthat
SystemRequirements
Enhances
URL	https://doi.org/10.1038/s41597-021-01095-3
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	phenomis_1.2.0.tar.gz
Windows Binary	phenomis_1.2.0.zip
macOS Binary (x86_64)	phenomis_1.2.0.tgz
macOS Binary (arm64)	phenomis_1.2.0.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