| annotationListToMatrix | Change annotation list to matrix |
| BHI | Biological Homogeneity Index |
| BSI | Biological Stability Index |
| clValid | Validate Cluster Results |
| clValid-class | Class "clValid" |
| clValid-internal | Internal clValid functions |
| connectivity | Connectivity Measure |
| dunn | Dunn Index |
| getRanksWeights | Extract ranks and weights from clValid object |
| mouse | Mouse Mesenchymal Cells |
| plot.sota | Plot Function for a SOTA Object |
| print.sota | Print Function for a SOTA Object |
| readAnnotationFile | Read in biological annotation files from external file |
| sota | Self-organizing Tree Algorithm (SOTA) |
| stability | Stability Measures |
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