![[R logo]](../../../doc/html/logo.jpg){kind=logo}
![[Up]](../../../doc/html/left.jpg)
![[Top]](../../../doc/html/up.jpg)
| annotationListToMatrix | generate relationship between genes and gene-sets |
| clusterMethods | Basic methods for a cogena object. |
| clusterMethods,cogena_methods | Basic methods for a cogena object. |
| clusterMethods-method | Basic methods for a cogena object. |
| clusters | Basic methods for a cogena object. |
| clusters,cogena_methods | Basic methods for a cogena object. |
| clusters-method | Basic methods for a cogena object. |
| cogena | co-expressed gene-set enrichment analysis |
| cogena-class | An S4 class to represent co-expressed gene-set enrichment analysis result. |
| corInCluster | Correlation in the cluster of a cogena object |
| corInCluster,cogena_methods | Correlation in the cluster of a cogena object |
| corInCluster-method | Correlation in the cluster of a cogena object |
| DEexprs | gene expression of DEG |
| enrichment | get the enrichment table from a cogena object. |
| enrichment,cogena_methods | get the enrichment table from a cogena object. |
| enrichment-method | get the enrichment table from a cogena object. |
| gene2set | generate relationship between genes and gene-sets |
| geneExpInCluster | Get gene names in each clusters and the expression profiling. |
| geneExpInCluster,cogena_methods | Get gene names in each clusters and the expression profiling. |
| geneExpInCluster-method | Get gene names in each clusters and the expression profiling. |
| geneInCluster | Get gene names in a certain cluster. |
| geneInCluster,cogena_methods | Get gene names in a certain cluster. |
| geneInCluster-method | Get gene names in a certain cluster. |
| gmt2list | read gmt file as a list |
| heatmapCluster | heatmap of gene expression profilings with cluster indication. |
| heatmapCluster-method | heatmap of gene expression profilings with cluster indication. |
| heatmapPEI | heatmap of the gene set enrichment from a cogena object. |
| heatmapPEI,cogena | heatmap of the gene set enrichment from a cogena object. |
| heatmapPEI-method | heatmap of the gene set enrichment from a cogena object. |
| heatmapPEI2 | heatmap of the gene set enrichment_score matrix directly |
| heatmapPEI2,cogena | heatmap of the gene set enrichment_score matrix directly |
| heatmapPEI2-method | heatmap of the gene set enrichment_score matrix directly |
| hubgeneInCluster | Show hub gene names in certain cluster. |
| hubgeneInCluster-method | Show hub gene names in certain cluster. |
| mat | Basic methods for a cogena object. |
| mat,cogena_methods | Basic methods for a cogena object. |
| mat-method | Basic methods for a cogena object. |
| nClusters | Basic methods for a cogena object. |
| nClusters,cogena_methods | Basic methods for a cogena object. |
| nClusters-method | Basic methods for a cogena object. |
| optCluster | get the best clustering methods and the number of clusters |
| optCluster,cogena | get the best clustering methods and the number of clusters |
| optCluster-method | get the best clustering methods and the number of clusters |
| PD | Parkinson's Disease dataset. |
| PD,DEexprs,sampleLabel,cogena_result | Parkinson's Disease dataset. |
| plot.sota | Self-organizing tree algorithm (SOTA) |
| print.sota | Self-organizing tree algorithm (SOTA) |
| sampleLabel | label of samples |
| sota | Self-organizing tree algorithm (SOTA) |
| summary-method | Basic methods for a cogena object. |