PAPi

This package is for version 3.7 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see PAPi.

Predict metabolic pathway activity based on metabolomics data


Bioconductor version: 3.7

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 (!require("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")
Applying PAPi PDF R Script
PAPi.pdf PDF
Reference Manual PDF

Details

biocViews MassSpectrometry, Metabolomics, Software
Version 1.20.0
In Bioconductor since BioC 2.12 (R-3.0) (11 years)
License GPL(>= 2)
Depends R (>= 2.15.2), svDialogs, KEGGREST
Imports
System Requirements
URL
See More
Suggests
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package PAPi_1.20.0.tar.gz
Windows Binary PAPi_1.20.0.zip
Mac OS X 10.11 (El Capitan) PAPi_1.20.0.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 https://bioconductor.org/packages/PAPi/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.7 Source Archive