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.

Author
Yue Deng, Rongjie Shao, Gang Wang and Yuanjun Sun
Date of publication
2015-07-28 08:03:42
Maintainer
Yue Deng <anfdeng@163.com>
License
GPL-2
Version
1.9

View on CRAN

Man pages

AASim
Compute Adamic-Adar Index Between Two Nodes in PPI Network
ComputeAllEvidences
Compute the Biological and Topological Similarities Between...
FNPre
Predict false negative interactions based on topological...
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-internal
Internal ppiPre objects
ppiPre-package
Predicting protein-protein interactions
RASim
Compute Resource Allocation Index Between Two Nodes in PPI...
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...
TopologicSims
Compute topological similarities from user input file

Files in this package

ppiPre
ppiPre/NAMESPACE
ppiPre/NEWS
ppiPre/R
ppiPre/R/SVMPredict.r
ppiPre/R/GOKEGGSims.r
ppiPre/R/TopologicSims.r
ppiPre/R/zzz.r
ppiPre/MD5
ppiPre/DESCRIPTION
ppiPre/man
ppiPre/man/ComputeAllEvidences.Rd
ppiPre/man/SVMTrain.Rd
ppiPre/man/TopologicSims.Rd
ppiPre/man/SVMPredict.Rd
ppiPre/man/GOKEGGSims.Rd
ppiPre/man/ppiPre-package.Rd
ppiPre/man/IntelliGOGeneSim.Rd
ppiPre/man/GOKEGGSimsFromFile.Rd
ppiPre/man/AASim.Rd
ppiPre/man/KEGGSim.Rd
ppiPre/man/TCSSGeneSim.Rd
ppiPre/man/FNPre.Rd
ppiPre/man/JaccardSim.Rd
ppiPre/man/RASim.Rd
ppiPre/man/ppiPre-internal.Rd