cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.
|Author||Zhilong Jia [aut, cre], Michael Barnes [aut]|
|Date of publication||None|
|Maintainer||Zhilong Jia <email@example.com>|
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...