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| ABIdata | Gene Expression Data Matrix |
| findReplicateGroups | Find Groups of Replicate Samples Within Dataset |
| fitGMM | Fitting Gaussian Mixture Models |
| fitRockeDurbin | Fit Rocke-Durbin Error Model |
| GESTr | Gene Expression State Transformation |
| getMonotonicConfidences | Ensure monotonicity of two-class gene expression state confidence assignments |
| getMonotonicConfidences_multiclass | Ensure monotonicity of multi-class gene expression state confidence assignments |
| mergeComponents | Merge GMM Components with Highly Overlapping Support |
| TranSAM | Gene Expression State Transformed Significance Analysis of Microarrays |