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| cnvset | Copy Number Variation (CNV) data |
| computePS | Computes the profile statistics |
| cptModel | Computes within and between gene feature profile statistics by feature and amongst features |
| cptPlot | Scatterplot representation of gene sets by change points |
| cptSlopeplot | Scatterplot representation of identified change points gene set slopes |
| exprset | Gene Variant (EXP) data |
| GISPA | Gene Integrates Set Profile Analysis |
| propBarplot | A plotting function for proportion by sample |
| stackedBarplot | A plotting function for each sample proportion |
| varset | Variant (VAR) data |