ibh: Interaction Based Homogeneity for Evaluating Gene Lists

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This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions.

Author
Kircicegi Korkmaz, Volkan Atalay, Rengul Cetin Atalay.
Date of publication
None
Maintainer
Kircicegi Korkmaz <e102771@ceng.metu.edu.tr>
License
GPL (>= 2)
Version
1.22.0

View on Bioconductor

Man pages

findEntry
Find the index of an entry in an interaction list
ibh
Calculate interaction based homogeneity for the given gene...
ibhBioGRID
Calculate interaction based homogeneity for a gene list...
ibhClusterEval
Evaluate clustering with interaction based homogeneity
ibhClusterEvalBioGRID
Evaluate clustering with interaction based homogeneity using...
ibhForMultipleGeneLists
Calculate interaction based homogeneity for multiple gene...
ibhForMultipleGeneListsBioGRID
Calculate interaction based homogeneity for multiple gene...
ibh-package
Interaction Based Homogeneity
readDirectedInteractionsFromCsv
Read directed interactions from csv and create the...
readUndirectedInteractionsFromCsv
Read undirected interactions from csv and create the...

Files in this package

ibh/DESCRIPTION
ibh/NAMESPACE
ibh/R
ibh/R/ibh-internal.R
ibh/R/ibh.R
ibh/build
ibh/build/vignette.rds
ibh/inst
ibh/inst/doc
ibh/inst/doc/ibh.R
ibh/inst/doc/ibh.Rnw
ibh/inst/doc/ibh.pdf
ibh/man
ibh/man/findEntry.Rd
ibh/man/ibh-package.Rd
ibh/man/ibh.Rd
ibh/man/ibhBioGRID.Rd
ibh/man/ibhClusterEval.Rd
ibh/man/ibhClusterEvalBioGRID.Rd
ibh/man/ibhForMultipleGeneLists.Rd
ibh/man/ibhForMultipleGeneListsBioGRID.Rd
ibh/man/readDirectedInteractionsFromCsv.Rd
ibh/man/readUndirectedInteractionsFromCsv.Rd
ibh/vignettes
ibh/vignettes/ibh.Rnw
ibh/vignettes/ibh.bib