Introduction | Obtaining the clustering | Obtaining Entity Attribute associations | Consolidating Entity-Attribute associations | Calculating the mutual information | Judging the clustering for selected uncertainty levels | References
Package: ClusterJudge 1.35.0
Adrian Pasculescu
ClusterJudge: Judging Quality of Clustering Methods using Mutual Information
ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation" and it appeared in Genome Research, vol. 12, pp1574-1581 (2002). See package?ClusterJudge for an overview.
Authors:
ClusterJudge_1.35.0.tar.gz
ClusterJudge_1.35.0.zip(r-4.7)ClusterJudge_1.35.0.zip(r-4.6)ClusterJudge_1.35.0.zip(r-4.5)
ClusterJudge_1.35.0.tgz(r-4.6-any)ClusterJudge_1.35.0.tgz(r-4.5-any)
ClusterJudge_1.35.0.tar.gz(r-4.7-any)ClusterJudge_1.35.0.tar.gz(r-4.6-any)
ClusterJudge_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ClusterJudge/json (API)
| # Install 'ClusterJudge' in R: |
| install.packages('ClusterJudge', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- mi.GO.Yeast - Precalculated mutual information between Gene Ontology attributes of Yeast genes
- Yeast.GO.assocs - Gene Ontology attributes associated to Yeast Gene entities
On BioConductor:ClusterJudge-1.35.0(bioc 3.24)ClusterJudge-1.34.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
softwarestatisticalmethodclusteringgeneexpressiongo
Last updated from:cd1c2d96c2. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 180 | ||
| linux-devel-x86_64 | OK | 288 | ||
| source / vignettes | OK | 245 | ||
| linux-release-x86_64 | OK | 262 | ||
| macos-release-arm64 | OK | 218 | ||
| macos-oldrel-arm64 | OK | 139 | ||
| windows-devel | OK | 178 | ||
| windows-release | OK | 189 | ||
| windows-oldrel | OK | 177 | ||
| wasm-release | OK | 168 |
Exports:attribute_mut_infclusterJudgeclusterJudge_z_scoreconsolidate_entity_attributedownload_Yeast_GO_mappingdownload_Yeast_Go_termsentities_attribute_statsvalidate_association
Dependencies:askpasscurldeldirhttrinfotheointerpjpegjsonlitelatticelatticeExtraMASSmimeopensslpngR6RColorBrewerRcppRcppEigensys
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Judging Quality of Clustering Methods using Mutual Information | ClusterJudge-package ClusterJudge |
| calculates the mutual information between each attribute of the entity.attribute pairs | attribute_mut_inf |
| judges clustering using an entity.attribute table | clusterJudge |
| calculates the `cluster judge` z-score | clusterJudge_z_score |
| removes the redundant attributes based on the mutual information between attributes | consolidate_entity_attribute |
| downloads the Gene Ontology attributes mapped to Yeast genes | download_Yeast_GO_mapping |
| downloads the description of Gene Ontology attributes | download_Yeast_Go_terms |
| presents basic statistics on the number of entities per attribute | entities_attribute_stats |
| precalculated mutual information between Gene Ontology attributes of Yeast genes | mi.GO.Yeast |
| validates the associations between entities and attributes | validate_association |
| Gene Ontology attributes associated to Yeast Gene entities | Yeast.GO.assocs |
