Package: BioNet 1.65.0

Marcus Dittrich

BioNet: Routines for the functional analysis of biological networks

This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.

Authors:Marcus Dittrich and Daniela Beisser

BioNet_1.65.0.tar.gz
BioNet_1.65.0.zip(r-4.5)BioNet_1.65.0.zip(r-4.4)BioNet_1.65.0.zip(r-4.3)
BioNet_1.65.0.tgz(r-4.4-any)BioNet_1.65.0.tgz(r-4.3-any)
BioNet_1.65.0.tar.gz(r-4.5-noble)BioNet_1.65.0.tar.gz(r-4.4-noble)
BioNet_1.65.0.tgz(r-4.4-emscripten)BioNet_1.65.0.tgz(r-4.3-emscripten)
BioNet.pdf |BioNet.html✨
BioNet/json (API)

Peer review:

On BioConductor:BioNet-1.65.0(bioc 3.20)BioNet-1.64.0(bioc 3.19)

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

bioconductor-package

42 exports 4.55 score 45 dependencies 2 dependents 40 mentions

Last updated 2 months agofrom:63db8f8d51

Exports:aggrPvalsbumOptimcompareNetworksconsensusScoresfbumfbumLLfdrThresholdfitBumModelgetCompScoresgetEdgeListhist.bumlargestComplargestScoreComploadNetwork.sifloadNetwork.tabmakeNetworkmapByVarpermutateNodespiUpperplot.bumplot3dModuleplotLLSurfaceplotModuleprint.bumreadHeinzGraphreadHeinzTreeresamplingPvaluesrmSelfLoopsrunFastHeinzrunHeinzsave3dModulesaveNetworkscanFDRscoreFunctionscoreNodesscoreOffsetsortedEdgeListsubNetworksummary.bumwriteHeinzwriteHeinzEdgeswriteHeinzNodes

Dependencies:AnnotationDbiaskpassBHBiobaseBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIfastmapGenomeInfoDbGenomeInfoDbDatagluegraphhttrigraphIRangesjsonliteKEGGRESTlatticelifecyclemagrittrMatrixmemoisemimeopensslpkgconfigplogrpngR6RBGLrlangRSQLiteS4VectorssysUCSC.utilsvctrsXVectorzlibbioc