Introduction | Functions
Package: ibh 1.61.0
Kircicegi Korkmaz
ibh: Interaction Based Homogeneity for Evaluating Gene Lists
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.
Authors:
ibh_1.61.0.tar.gz
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ibh_1.61.0.tgz(r-4.6-any)ibh_1.61.0.tgz(r-4.5-any)
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ibh_1.61.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
ibh/json (API)
| # Install 'ibh' in R: |
| install.packages('ibh', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:ibh-1.61.0(bioc 3.24)ibh-1.60.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
qualitycontroldataimportgraphandnetworknetworkenrichment
Last updated from:5bf7aef13f. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 133 | ||
| linux-devel-x86_64 | NOTE | 119 | ||
| source / vignettes | OK | 227 | ||
| linux-release-x86_64 | NOTE | 161 | ||
| macos-release-arm64 | NOTE | 99 | ||
| macos-oldrel-arm64 | NOTE | 97 | ||
| windows-devel | NOTE | 85 | ||
| windows-release | NOTE | 84 | ||
| windows-oldrel | NOTE | 95 | ||
| wasm-release | OK | 94 |
Exports:findEntryibhibhBioGRIDibhClusterEvalibhClusterEvalBioGRIDibhForMultipleGeneListsibhForMultipleGeneListsBioGRIDreadDirectedInteractionsFromCsvreadUndirectedInteractionsFromCsv
Dependencies:simpIntLists
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Interaction Based Homogeneity | ibh-package |
| Find the index of an entry in an interaction list | findEntry |
| Calculate interaction based homogeneity for the given gene list according to the interaction list | ibh |
| Calculate interaction based homogeneity for a gene list according to the BioGRID Interactions | ibhBioGRID |
| Evaluate clustering with interaction based homogeneity | ibhClusterEval |
| Evaluate clustering with interaction based homogeneity using BioGRID Interactions | ibhClusterEvalBioGRID |
| Calculate interaction based homogeneity for multiple gene lists according to the interaction list | ibhForMultipleGeneLists |
| Calculate interaction based homogeneity for multiple gene lists according to the BioGRID Interactions | ibhForMultipleGeneListsBioGRID |
| Read directed interactions from csv and create the interaction list | readDirectedInteractionsFromCsv |
| Read undirected interactions from csv and create the interaction list | readUndirectedInteractionsFromCsv |