ppiPre: Predict Protein-Protein Interactions Based on Functional and Topological Similarities

Computing similarities between proteins based on their GO annotation, KEGG annotation and PPI network topology. It integrates seven features (TCSS, IntelliGO, Wang, KEGG, Jaccard, RA and AA) to predict PPIs using an SVM classifier. Some internal functions to calculate GO semantic similarities are re-used from R package GOSemSim authored by Guangchuang Yu.

Install the latest version of this package by entering the following in R:
install.packages("ppiPre")
AuthorYue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun
Date of publication2015-07-28 08:03:42
MaintainerYue Deng <anfdeng@163.com>
LicenseGPL-2
Version1.9

View on CRAN

Functions

AASim Man page
CheckAnnotationPackage Man page
ComputeAllEvidences Man page
FNPre Man page
GetGOMap Man page
GetGOParents Man page
GetLatestCommonAncestor Man page
GetOntology Man page
GOKEGGSims Man page
GOKEGGSimsFromFile Man page
.initial Man page
IntelliGOComputeEiEj Man page
IntelliGOGeneSim Man page
IntelliGOGetDepth Man page
IntelliGOGetParents Man page
IntelliGOGOSim Man page
IntelliGOInverseAnnotationFrequency Man page
JaccardSim Man page
KEGGSim Man page
ppiPre Man page
ppiPre-package Man page
RASim Man page
SVMPredict Man page
SVMTrain Man page
TCSSCompute_ICA Man page
TCSSGeneSim Man page
TCSSGetAncestors Man page
TCSSGetChildren Man page
TCSSGetOffsprings Man page
TCSSGoSim Man page
TopologicSims Man page

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

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