Path2PPI: Prediction of pathway-related protein-protein interaction networks

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Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.

Author
Oliver Philipp [aut, cre], Ina Koch [ctb]
Date of publication
None
Maintainer
Oliver Philipp <contact@oliverphilipp.info>
License
GPL (>= 2)
Version
1.4.0
URLs

View on Bioconductor

Man pages

addReference
Add reference species
ai
Data set to predict autophagy induction in _Podospora...
getHybridNetwork
Get hybrid network of the predicted PPI
getPPI
Get predicted PPI
homologyScore
Computes homology scores
Path2PPI
Class '"Path2PPI"'
plot.Path2PPI
Plots the predicted PPI
predictPPI
Prediction of the PPI
removeReference
Remove reference species
showInteraction
Information about an interaction
showReferences
Information about reference species

Files in this package

Path2PPI/CITATION
Path2PPI/DESCRIPTION
Path2PPI/NAMESPACE
Path2PPI/NEWS
Path2PPI/R
Path2PPI/R/AllClasses.R
Path2PPI/R/AllGenerics.R
Path2PPI/R/initialize-methods.R
Path2PPI/R/private_methods.R
Path2PPI/R/public_methods.R
Path2PPI/R/show-methods.R
Path2PPI/build
Path2PPI/build/vignette.rds
Path2PPI/data
Path2PPI/data/ai.rda
Path2PPI/inst
Path2PPI/inst/doc
Path2PPI/inst/doc/Path2PPI-tutorial.R
Path2PPI/inst/doc/Path2PPI-tutorial.Rmd
Path2PPI/inst/doc/Path2PPI-tutorial.html
Path2PPI/inst/unitTests
Path2PPI/inst/unitTests/test_various.R
Path2PPI/man
Path2PPI/man/Path2PPI.Rd
Path2PPI/man/addReference.Rd
Path2PPI/man/ai.Rd
Path2PPI/man/getHybridNetwork.Rd
Path2PPI/man/getPPI.Rd
Path2PPI/man/homologyScore.Rd
Path2PPI/man/plot.Path2PPI.Rd
Path2PPI/man/predictPPI.Rd
Path2PPI/man/removeReference.Rd
Path2PPI/man/showInteraction.Rd
Path2PPI/man/showReferences.Rd
Path2PPI/tests
Path2PPI/tests/runTests.R
Path2PPI/vignettes
Path2PPI/vignettes/Path2PPI-tutorial.Rmd
Path2PPI/vignettes/figures
Path2PPI/vignettes/figures/algorithm.png