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phoenics (version 0.6)

Pathways Longitudinal and Differential Analysis in Metabolomics

Description

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) is based on a Principal Component Analysis step and on a linear mixed model. Automatic query of metabolic pathways is also implemented.

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Version

Install

install.packages('phoenics')

Monthly Downloads

258

Version

0.6

License

GPL-3

Maintainer

Remi Servien

Last Published

August 19th, 2025

Functions in phoenics (0.6)

from_ASICS_to_PHOENICS

Prepare quantification data from ASICS outputs
pathwayRes

Class pathwayRes
pathway_search

Query KEGG pathways for a given set of metabolites
test_pathway

Pathway differential analysis based on longitudinal metabolomics data
overlap_coefficient

Calculate overlap coefficient between pathways
MTBLS422

Dataset "MTBLS422"