Package: PPInfer 1.33.0

Dongmin Jung

PPInfer: Inferring functionally related proteins using protein interaction networks

Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.

Authors:Dongmin Jung, Xijin Ge

PPInfer_1.33.0.tar.gz
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PPInfer.pdf |PPInfer.html
PPInfer/json (API)
NEWS

# Install 'PPInfer' in R:
install.packages('PPInfer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:PPInfer-1.33.0(bioc 3.21)PPInfer-1.32.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

softwarestatisticalmethodnetworkgraphandnetworkgenesetenrichmentnetworkenrichmentpathways

4.48 score 1 packages 4 scripts 428 downloads 10 exports 106 dependencies

Last updated 5 months agofrom:d4d24bc527. Checks:4 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKMar 30 2025
R-4.5-winOKMar 30 2025
R-4.5-macOKMar 30 2025
R-4.5-linuxOKMar 30 2025
R-4.4-winNOTEMar 30 2025
R-4.4-macNOTEMar 30 2025
R-4.4-linuxNOTEMar 30 2025
R-4.3-winNOTEMar 30 2025
R-4.3-macNOTEMar 30 2025

Exports:enrich.netGSEA.barplotnet.infernet.infer.STnet.kernelORAORA.barplotppi.infer.humanppi.infer.mouseself.train.kernel

Dependencies:AnnotationDbiaskpassBHBiobaseBiocFileCacheBiocGenericsBiocParallelbiomaRtBiostringsbitbit64bitopsblobcachemcaToolschronclicodetoolscolorspacecowplotcpp11crayoncurldata.tableDBIdbplyrdigestdplyrfansifarverfastmapfastmatchfgseafilelockformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegplotsgraphgsubfngtablegtoolshashhmshttrhttr2igraphIRangesisobandjsonliteKEGGRESTkernlabKernSmoothlabelinglambda.rlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrplotrixplyrpngprettyunitsprogressprotopurrrR6rappdirsRColorBrewerRcpprlangRSQLiteS4VectorsscalessnowsqldfSTRINGdbstringistringrsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrxml2XVectoryeastExpData

User manual

Rendered fromPPInfer.Rnwusingutils::Sweaveon Mar 30 2025.

Last update: 2020-02-03
Started: 2017-04-18