| PPInfer-package | Inferring functionally related proteins using protein interaction networks |
| enrich.net | Visualize network for the functional enrichment analysis |
| GSEA.barplot | Visualize the gene set enrichment analysis |
| net.infer | Inferring functionally related proteins using networks |
| net.infer.ST | Inferring functionally related proteins with self training |
| net.kernel | Kernel matrix for a graph |
| ORA | Over-representation Analysis |
| ORA.barplot | Visualize the over-representation analysis |
| ppi.infer.human | Inferring functionally related proteins using protein networks for human |
| ppi.infer.mouse | Inferring functionally related proteins using protein networks for mouse |
| PPInfer | Inferring functionally related proteins using protein interaction networks |
| self.train.kernel | Self training for a kernel matrix |