PAPi

DOI: 10.18129/B9.bioc.PAPi    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see PAPi.

Predict metabolic pathway activity based on metabolomics data

Bioconductor version: 3.8

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 gmail.com>

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

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("PAPi")

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("PAPi")

 

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

Details

biocViews ImmunoOncology, MassSpectrometry, Metabolomics, Software
Version 1.22.1
In Bioconductor since BioC 2.12 (R-3.0) (6 years)
License GPL(>= 2)
Depends R (>= 2.15.2), svDialogs, KEGGREST
Imports
LinkingTo
Suggests
SystemRequirements
Enhances
URL
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 PAPi_1.22.1.tar.gz
Windows Binary PAPi_1.22.1.zip
Mac OS X 10.11 (El Capitan) PAPi_1.22.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/PAPi
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/PAPi
Package Short Url http://bioconductor.org/packages/PAPi/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: