ibh: Interaction Based Homogeneity for Evaluating Gene Lists
Version 1.24.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorKircicegi Korkmaz, Volkan Atalay, Rengul Cetin Atalay.
Bioconductor views DataImport GraphAndNetwork NetworkEnrichment QualityControl
Date of publicationNone
MaintainerKircicegi Korkmaz <e102771@ceng.metu.edu.tr>
LicenseGPL (>= 2)
Version1.24.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("ibh")

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...

Functions

findEntry Man page Source code
ibh Man page Source code
ibh-package Man page
ibhBioGRID Man page Source code
ibhClusterEval Man page Source code
ibhClusterEvalBioGRID Man page Source code
ibhForMultipleGeneLists Man page Source code
ibhForMultipleGeneListsBioGRID Man page Source code
readDirectedInteractionsFromCsv Man page Source code
readUndirectedInteractionsFromCsv Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/ibh-internal.R
R/ibh.R
build
build/vignette.rds
inst
inst/doc
inst/doc/ibh.R
inst/doc/ibh.Rnw
inst/doc/ibh.pdf
man
man/findEntry.Rd
man/ibh-package.Rd
man/ibh.Rd
man/ibhBioGRID.Rd
man/ibhClusterEval.Rd
man/ibhClusterEvalBioGRID.Rd
man/ibhForMultipleGeneLists.Rd
man/ibhForMultipleGeneListsBioGRID.Rd
man/readDirectedInteractionsFromCsv.Rd
man/readUndirectedInteractionsFromCsv.Rd
vignettes
vignettes/ibh.Rnw
vignettes/ibh.bib
ibh documentation built on May 20, 2017, 9:47 p.m.