Package: ClassDiscovery 3.4.5

Kevin R. Coombes

ClassDiscovery: Classes and Methods for "Class Discovery" with Microarrays or Proteomics

Defines the classes used for "class discovery" problems in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class discovery primarily consists of unsupervised clustering methods with attempts to assess their statistical significance.

Authors:Kevin R. Coombes

ClassDiscovery_3.4.5.tar.gz
ClassDiscovery_3.4.5.zip(r-4.5)ClassDiscovery_3.4.5.zip(r-4.4)ClassDiscovery_3.4.5.zip(r-4.3)
ClassDiscovery_3.4.5.tgz(r-4.4-any)ClassDiscovery_3.4.5.tgz(r-4.3-any)
ClassDiscovery_3.4.5.tar.gz(r-4.5-noble)ClassDiscovery_3.4.5.tar.gz(r-4.4-noble)
ClassDiscovery_3.4.5.tgz(r-4.4-emscripten)ClassDiscovery_3.4.5.tgz(r-4.3-emscripten)
ClassDiscovery.pdf |ClassDiscovery.html✨
ClassDiscovery/json (API)
NEWS

# Install 'ClassDiscovery' in R:

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

Bug tracker:https://r-forge.r-project.org/projects/oompa

On CRAN:

27 exports 3.88 score 6 dependencies 9 dependents 13 mentions 86 scripts 2.4k downloads

Last updated 3 days agofrom:188f1924ef. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 05 2024
R-4.5-win	OK	Sep 05 2024
R-4.5-linux	OK	Sep 05 2024
R-4.4-win	OK	Sep 05 2024
R-4.4-mac	OK	Sep 05 2024
R-4.3-win	OK	Sep 05 2024
R-4.3-mac	OK	Sep 05 2024

Exports:as.data.frame aspectHeatmap BootstrapClusterTest cluster3 cutHclust cutKmeans cutPam cutRepeatedKmeans distanceMatrix GenePCA hist identify image mahalanobisQC Mosaic PCanova pcc PerturbationClusterTest plot plotColoredClusters pltree predict repeatedKmeans SamplePCA screeplot summary text

Dependencies:Biobase BiocGenerics cluster mclust oompaBase oompaData

OOMPA ClassDiscovery

Rendered fromoompa-cd.Rnwusingutils::Sweaveon Sep 05 2024.

Last update: 2014-02-10
Started: 2014-02-10

OOMPA Mahalanobis Distance

Rendered frommaha-test.Rnwusingutils::Sweaveon Sep 05 2024.

Last update: 2014-02-10
Started: 2014-02-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Heatmap with control over the aspect ratio	aspectHeatmap
Class "BootstrapClusterTest"	BootstrapClusterTest BootstrapClusterTest-class summary,BootstrapClusterTest-method
Cluster a Dataset Three Ways	cluster3
Class "ClusterTest"	ClusterTest ClusterTest-class hist,ClusterTest-method image,ClusterTest-method summary,ClusterTest-method
Distance Matrix Computation	distanceMatrix
Class "GenePCA"	GenePCA GenePCA-class plot,GenePCA,missing-method
Class "hclust"	hclust-class
Get the List of Classes From A Clustering Algorithm	cutHclust cutKmeans cutPam cutRepeatedKmeans repeatedKmeans
Using Mahalanobis Distance and PCA for Quality Control	mahalanobisQC
Class "Mosaic"	Mosaic Mosaic-class plot,Mosaic,missing-method pltree,Mosaic-method summary,Mosaic-method
Class "PCanova"	PCanova PCanova-class plot,PCanova,missing-method pltree,PCanova-method summary,PCanova-method
The PerturbationClusterTest Class	PerturbationClusterTest PerturbationClusterTest-class summary,PerturbationClusterTest-method
Plot Dendrograms with Color-Coded Labels	pcc plotColoredClusters
Class "SamplePCA"	identify,SamplePCA-method plot,SamplePCA,missing-method predict,SamplePCA-method SamplePCA SamplePCA-class screeplot,SamplePCA-method summary,SamplePCA-method text,SamplePCA-method