| assign_colorsAnnotation | Assing Colors to Class |
| Chow_GeneExpData | Chow gene expression data |
| Chow_MetaboliteData | Chow metabolite data |
| Compare_Triplets | Compare triplets |
| Compare_VertexClasses_sharedEdgeFeatures | Table VertexClass pairs of shared Edge Features |
| CoNI | Correlation guided Network Integration |
| CoNIResultsHFDToy | Toy data HFD results |
| CoNIResults_Chow | CoNI Results Chow |
| CoNIResults_HFD | CoNI Results HFD |
| createBipartiteGraph | Bipartite Network |
| create_edgeFBarplot | Vertex-class pairs profile of one shared edge feature |
| create_GlobalBarplot | Vertex-class pairs profile of shared features |
| create_stackedGlobalBarplot_perTreatment | Stacked Global Barplot (One treatment) |
| find_localControllingFeatures | Find local controlling features |
| GeneExpToy | Toy data gene expression |
| generate_network | Create network |
| getstackedGlobalBarplot_and_Grid | Stacked Global Barplot Side-by-side (two treatments) |
| getVertexsPerEdgeFeature | Vertex Class profile per edge feature (one treatment) |
| getVertexsPerEdgeFeature_and_Grid | Vertex-Class profile per edge feature Side-by-Side (two treatments) |
| HFD_GeneExpData | HFD gene expression data |
| HFD_MetaboliteData | HFD metabolite data |
| MetaboExpToy | Toy data metabolite expression |
| MetaboliteAnnotation | Metabolite Annotation |
| MetColorTable | Toy data annotation |
| NetStats | Network Statistics |
| plotPcorvsCor | Correlation vs Partial correlation |
| tableLCFs_VFs | Table local controlling edge features and vertex pairs |
| top_n_LF_byMagnitude | Linker Features by magnitude of effect |
| VertexClassesSharedGenes_HFDvsChow | Toy data comparison treatments |