Man pages for zhilongjia/cogena
co-expressed gene-set enrichment analysis
| AllGeneSymbols | All the gene symbols |
| clEnrich | Gene set enrichment for clusters |
| clEnrich_one | Gene set enrichment for clusters (for one clustering method... |
| clusterMethods | Basic methods for a genecl object. |
| coExp | co-expressed gene-set enrichment analysis |
| cogena_class | An S4 class to represent co-expressed gene-set enrichment... |
| cogena_package | Co-expressed gene set enrichment analysis |
| corInCluster | Correlation in the cluster of a cogena object |
| DEexprs | gene expression of DEG |
| enrichment | get the enrichment table from a cogena object. |
| gene2set | generate relationship between genes and gene-sets |
| genecl_class | An S4 class to represent co-expressed gene |
| geneclusters | geneclusters: get the cluster information of a certain... |
| geneExpInCluster | Get gene names in each clusters and the expression profiling. |
| geneInCluster | Get gene names in a certain cluster. |
| gmt2list | read gmt file as a list |
| gmtlist2file | write gmt list into gmt file |
| heatmap.3 | heatmap.3 An improved heatmap plotting |
| heatmapCluster | heatmap of gene expression profilings with cluster... |
| heatmapCmap | heatmap designed for for CMap gene set only |
| heatmapPEI | heatmap of the gene set enrichment from a cogena object. |
| mat | mat: get the original data from a genecl object. |
| nClusters | nClusters: get the number of clusters from a genecl object. |
| pClusters | paralleled clustering |
| PEI | Significance of Gene sets enrichment. |
| Psoriasis | Psoriasis dataset. |
| sampleLabel | label of samples |
| show | show: show the class of cogena or genecl object |
| sota | Self-organizing tree algorithm (SOTA) |
| summary | summary: a summary of a genecl object. |
| upDownGene | Show up or down-regualted genes for a clustering method and... |
