PAPi: Predict metabolic pathway activity based on metabolomics data

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PAPi")
AuthorRaphael Aggio
Bioconductor views MassSpectrometry Metabolomics
Date of publicationNone
MaintainerRaphael Aggio <raphael.aggio@gmail.com>
LicenseGPL(>= 2)
Version1.16.0

View on Bioconductor

Files

DESCRIPTION
NAMESPACE
R
R/addKeggCodes.R R/buildDatabase.R R/papi.R R/papiHtest.R R/papiLine.R
build
build/vignette.rds
data
data/keggLibrary.rda
data/metabolomicsData.rda
data/papiData.rda
data/papiResults.rda
inst
inst/databases
inst/databases/default
inst/databases/default/COMPbase.csv
inst/databases/default/PATHbase.csv
inst/doc
inst/doc/PAPi.pdf
inst/doc/PAPiPackage.R
inst/doc/PAPiPackage.Rnw
inst/doc/PAPiPackage.pdf
man
man/PAPi-package.Rd man/addKeggCodes.Rd man/buildDatabase.Rd man/keggLibrary.Rd man/metabolomicsData.Rd man/papi.Rd man/papiData.Rd man/papiHtest.Rd man/papiLine.Rd man/papiResults.Rd
unitTests
unitTests/test.addKeggCodes.R unitTests/test.papiHtest.R unitTests/test.papiLine.R
vignettes
vignettes/PAPi.pdf
vignettes/PAPiPackage.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.