Package: ClusterJudge 1.29.0

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:Adrian Pasculescu

ClusterJudge_1.29.0.tar.gz
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ClusterJudge_1.29.0.tgz(r-4.4-any)ClusterJudge_1.29.0.tgz(r-4.3-any)
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ClusterJudge.pdf |ClusterJudge.html✨
ClusterJudge/json (API)
NEWS

# Install 'ClusterJudge' in R:

install.packages('ClusterJudge', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

Yeast.GO.assocs - Gene Ontology attributes associated to Yeast Gene entities
mi.GO.Yeast - Precalculated mutual information between Gene Ontology attributes of Yeast genes

On BioConductor:ClusterJudge-1.29.0(bioc 3.21)ClusterJudge-1.28.0(bioc 3.20)

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

software statisticalmethod clustering geneexpression go

3.30 score 3 scripts 213 downloads 1 mentions 9 exports 19 dependencies

Last updated 2 months agofrom:e8c9f1db5a. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 29 2024
R-4.5-win	OK	Nov 29 2024
R-4.5-linux	OK	Nov 29 2024
R-4.4-win	OK	Nov 29 2024
R-4.4-mac	OK	Nov 29 2024
R-4.3-win	OK	Nov 29 2024
R-4.3-mac	OK	Nov 29 2024

Exports:attribute_mut_inf clusterJudge clusterJudge_z_score consolidate_entity_attribute convert_Yeast_SGDId_2_systematic download_Yeast_GO_mapping download_Yeast_Go_terms entities_attribute_stats validate_association

Dependencies:askpass curl deldir httr infotheo interp jpeg jsonlite lattice latticeExtra MASS mime openssl png R6 RColorBrewer Rcpp RcppEigen sys

ClusterJudge

Adrian Pasculescu

Rendered fromClusterJudge-intro.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2019-04-17
Started: 2017-06-14

Citation

Development and contributors

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
converts the SGD Gene Id into the systematic name of the gene	convert_Yeast_SGDId_2_systematic
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