Predict Protein-Protein Interactions Based on Functional and Topological Similarities

Documentation for package ‘ppiPre’ version 1.9

ppiPre-package	Predicting protein-protein interactions
AASim	Compute Adamic-Adar Index Between Two Nodes in PPI Network
ComputeAllEvidences	Compute the Biological and Topological Similarities Between Protein Pairs
FNPre	Predict false negative interactions based on topological similarities
GOKEGGSims	GO- and KEGG- based Similarities Between two Genes
GOKEGGSimsFromFile	GO- and KEGG- based Similarities Between two Genes
IntelliGOGeneSim	IntelliGO Semantic Similarity Between two Genes
JaccardSim	Compute Jaccard Index Between Two Nodes in PPI Network
KEGGSim	KEGG Semantic Similarity Between two Genes
ppiPre	Predicting protein-protein interactions
RASim	Compute Resource Allocation Index Between Two Nodes in PPI Network
SVMPredict	Predict false interactions using a training set
SVMTrain	Using Golden Standard Data Sets to Train an SVM Classifier
TCSSGeneSim	Topological Clustering Semantic Similarity(TCSS) Between two Genes
TopologicSims	Compute topological similarities from user input file