| apply.scaling | Apply scaling factors | 
| calculate.cis.matrix | Calculate consensus integrative correlation matrix | 
| calculate.integrative.similarity.matrix | Calculate integrative similarity matrix | 
| calculate.scaling | Calculate scaling factors | 
| cluster.patients | Clustering to find patient subtypes | 
| combine.integrative.features | Combine iSubGen integrative features | 
| create.autoencoder | Create an autoencoder for dimensionality reduction | 
| create.autoencoder.irf.matrix | Create matrix of independent reduced features | 
| load.molecular.aberration.data | Load molecular aberration data | 
| read.scaling.factors | Read scaling factors from file | 
| write.scaling.factors | Write scaling factors to file |