cogena: co-expressed gene-set enrichment analysis

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.

AuthorZhilong Jia [aut, cre], Michael Barnes [aut]
Date of publicationNone
MaintainerZhilong Jia <zhilongjia@gmail.com>
LicenseLGPL-3
Version1.8.0
https://github.com/zhilongjia/cogena

View on Bioconductor

Man pages

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...

Files in this package

cogena/DESCRIPTION
cogena/NAMESPACE
cogena/R
cogena/R/Class_methods.R cogena/R/PEI.R cogena/R/clEnrich.R cogena/R/clEnrich_one.R cogena/R/coExp.R cogena/R/cogena.R cogena/R/cogena_class.R cogena/R/corInCluster.R cogena/R/dist_class.R cogena/R/enrichment.R cogena/R/gene2set.R cogena/R/geneExpInCluster.R cogena/R/geneInCluster.R cogena/R/genecl_class.R cogena/R/gmt2list.R cogena/R/gmtlist2file.R cogena/R/heatmap.3.R cogena/R/heatmapCluster.R cogena/R/heatmapCmap.R cogena/R/heatmapPEI.R cogena/R/pClusters.R cogena/R/sota.R cogena/R/upDownGene.R
cogena/README.md
cogena/build
cogena/build/vignette.rds
cogena/data
cogena/data/AllGeneSymbols.RData
cogena/data/Psoriasis.RData
cogena/data/datalist
cogena/inst
cogena/inst/NEWS.Rd
cogena/inst/doc
cogena/inst/doc/cogena-vignette_html.R
cogena/inst/doc/cogena-vignette_html.Rmd
cogena/inst/doc/cogena-vignette_html.html
cogena/inst/doc/cogena-vignette_pdf.R
cogena/inst/doc/cogena-vignette_pdf.Rmd
cogena/inst/doc/cogena-vignette_pdf.pdf
cogena/inst/extdata
cogena/inst/extdata/CmapDn100.gmt.xz
cogena/inst/extdata/CmapUp100.gmt.xz
cogena/inst/extdata/c2.cp.biocarta.v5.0.symbols.gmt.xz
cogena/inst/extdata/c2.cp.kegg.v5.0.symbols.gmt.xz
cogena/inst/extdata/c2.cp.reactome.v5.0.symbols.gmt.xz
cogena/inst/extdata/c2.cp.v5.0.symbols.gmt.xz
cogena/inst/extdata/c5.bp.v5.0.symbols.gmt.xz
cogena/inst/extdata/c5.mf.v5.0.symbols.gmt.xz
cogena/inst/figure
cogena/inst/figure/Cogena_workflow.png
cogena/man
cogena/man/AllGeneSymbols.Rd cogena/man/DEexprs.Rd cogena/man/PEI.Rd cogena/man/Psoriasis.Rd cogena/man/clEnrich.Rd cogena/man/clEnrich_one.Rd cogena/man/clusterMethods.Rd cogena/man/coExp.Rd cogena/man/cogena_class.Rd cogena/man/cogena_package.Rd cogena/man/corInCluster.Rd cogena/man/enrichment.Rd cogena/man/gene2set.Rd cogena/man/geneExpInCluster.Rd cogena/man/geneInCluster.Rd cogena/man/genecl_class.Rd cogena/man/geneclusters.Rd cogena/man/gmt2list.Rd cogena/man/gmtlist2file.Rd cogena/man/heatmap.3.Rd cogena/man/heatmapCluster.Rd cogena/man/heatmapCmap.Rd cogena/man/heatmapPEI.Rd cogena/man/mat.Rd cogena/man/nClusters.Rd cogena/man/pClusters.Rd cogena/man/sampleLabel.Rd cogena/man/show.Rd cogena/man/sota.Rd cogena/man/summary.Rd cogena/man/upDownGene.Rd
cogena/tests
cogena/tests/testthat
cogena/vignettes
cogena/vignettes/Cogena_workflow.png
cogena/vignettes/cogena-vignette_html.Rmd
cogena/vignettes/cogena-vignette_pdf.Rmd
cogena/vignettes/custom.css

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