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| clusterDist | clusterDist |
| ctlSeparatn | Calculate control separation |
| distToNeg | distToNeg |
| enrichAnalysis | enrichAnalysis |
| PDMByFactorAnalysis | Calculate phenotypic distance matrix by factor analysis |
| PDMByKS | Compute phenotypic distance matrix by Kolmogorov-Smirnov statistics |
| PDMBySvmAccuracy | Compute phenotypic distance matrix by SVM classification accuracy |
| PDMBySvmWeightVector | Compute phenotypic distance matrix by SVM weight vector |
| PDMByWellAvg | Compute phenotypic distance matrix with well features |
| repCorr | repCorr |
| repDistRank | repDistRank |