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.

Author
Raphael Aggio
Date of publication
None
Maintainer
Raphael Aggio <raphael.aggio@gmail.com>
License
GPL(>= 2)
Version
1.14.0

View on Bioconductor

Man pages

addKeggCodes
In a data frame, it substitutes the name of compounds by...
buildDatabase
Build a local database containing the required information...
keggLibrary
An example of the library mapping name of compounds to their...
metabolomicsData
An example of metabolomics data set used by 'addKeggCodes'.
papi
papi - Pathway Activity Profiling
papiData
An example of the data frame produced by 'addKeggCodes' and...
papiHtest
Apply ANOVA or t-test to results produced by 'papi'.
papiLine
papiLine generates a line graph of results obtained using...
PAPi-package
Pathway Activity Profiling
papiResults
An example of the data frame produced by 'papi'.

Files in this package

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