Path2PPI: Prediction of pathway-related protein-protein interaction networks
Version 1.6.0

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.

AuthorOliver Philipp [aut, cre], Ina Koch [ctb]
Bioconductor views Network NetworkInference Pathways Proteomics SystemsBiology
Date of publicationNone
MaintainerOliver Philipp <contact@oliverphilipp.info>
LicenseGPL (>= 2)
Version1.6.0
URL http://www.bioinformatik.uni-frankfurt.de/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Path2PPI")

Getting started

Path2PPI - Tutorial, example and the algorithm"

Popular man pages

ai: Data set to predict autophagy induction in _Podospora...
getHybridNetwork: Get hybrid network of the predicted PPI
homologyScore: Computes homology scores
Path2PPI: Class '"Path2PPI"'
predictPPI: Prediction of the PPI
showInteraction: Information about an interaction
showReferences: Information about reference species
See all...

All man pages Function index File listing

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

Functions

Files

CITATION
DESCRIPTION
NAMESPACE
NEWS
R
R/AllClasses.R
R/AllGenerics.R
R/initialize-methods.R
R/private_methods.R
R/public_methods.R
R/show-methods.R
build
build/vignette.rds
data
data/ai.rda
inst
inst/doc
inst/doc/Path2PPI-tutorial.R
inst/doc/Path2PPI-tutorial.Rmd
inst/doc/Path2PPI-tutorial.html
inst/unitTests
inst/unitTests/test_various.R
man
man/Path2PPI.Rd
man/addReference.Rd
man/ai.Rd
man/getHybridNetwork.Rd
man/getPPI.Rd
man/homologyScore.Rd
man/plot.Path2PPI.Rd
man/predictPPI.Rd
man/removeReference.Rd
man/showInteraction.Rd
man/showReferences.Rd
tests
tests/runTests.R
vignettes
vignettes/Path2PPI-tutorial.Rmd
vignettes/figures
vignettes/figures/algorithm.png
Path2PPI documentation built on May 20, 2017, 9:35 p.m.

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