phoenics: Pathways Longitudinal and Differential Analysis in Metabolomics

Perform a differential analysis at pathway level based on metabolite quantifications and information on pathway metabolite composition. The method, described in Guilmineau et al (2025) <doi:10.1186/s12859-025-06118-z> is based on a Principal Component Analysis step and on a linear mixed model. Automatic query of metabolic pathways is also implemented.

Version: 0.6
Depends: R (≥ 4.0.0)
Imports: lme4, blme, tibble, FactoMineR, factoextra, tidyr, stats
Suggests: knitr, KEGGREST
Published: 2025-08-19
DOI: 10.32614/CRAN.package.phoenics
Author: Camille Guilmineau [aut], Remi Servien ORCID iD [aut, cre], Nathalie Vialaneix ORCID iD [aut]
Maintainer: Remi Servien <remi.servien at inrae.fr>
BugReports: https://forge.inrae.fr/panoramics/phoenics/-/issues
License: GPL-3
URL: https://forge.inrae.fr/panoramics/phoenics
NeedsCompilation: no
Language: en-US
Citation: phoenics citation info
Materials: NEWS
CRAN checks: phoenics results

Documentation:

Reference manual: phoenics.html , phoenics.pdf
Vignettes: Introduction to phoenics (source, R code)

Downloads:

Package source: phoenics_0.6.tar.gz
Windows binaries: r-devel: phoenics_0.6.zip, r-release: phoenics_0.6.zip, r-oldrel: phoenics_0.6.zip
macOS binaries: r-release (arm64): phoenics_0.5.tgz, r-oldrel (arm64): phoenics_0.5.tgz, r-release (x86_64): phoenics_0.6.tgz, r-oldrel (x86_64): phoenics_0.6.tgz
Old sources: phoenics archive

Linking:

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