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. |