DOI: 10.18129/B9.bioc.PAPi    

This is the development version of PAPi; for the stable release version, see PAPi.

Predict metabolic pathway activity based on metabolomics data

Bioconductor version: Development (3.9)

The Pathway Activity Profiling - PAPi - is an R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. See Aggio, R.B.M; Ruggiero, K. and Villas-Boas, S.G. (2010) - Pathway Activity Profiling (PAPi): from metabolite profile to metabolic pathway activity. Bioinformatics.

Author: Raphael Aggio

Maintainer: Raphael Aggio <raphael.aggio at>

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


To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
BiocManager::install("PAPi", version = "3.9")

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:



PDF R Script Applying PAPi
PDF PAPi.pdf
PDF   Reference Manual


biocViews MassSpectrometry, Metabolomics, Software
Version 1.23.0
In Bioconductor since BioC 2.12 (R-3.0) (5.5 years)
License GPL(>= 2)
Depends R (>= 2.15.2), svDialogs, KEGGREST
Depends On Me
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Follow Installation instructions to use this package in your R session.

Source Package PAPi_1.23.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) PAPi_1.23.0.tgz
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