cogena: co-expressed gene-set enrichment analysis

Share:

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 <zhilongjia@gmail.com>
License
LGPL-3
Version
1.8.0
URLs

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