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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cogena")
AuthorZhilong Jia [aut, cre], Michael Barnes [aut]
Bioconductor views Clustering DataImport DataRepresentation GO GeneExpression GeneSetEnrichment KEGG Microarray Pathways Sequencing SystemsBiology Visualization
Date of publicationNone
MaintainerZhilong Jia <zhilongjia@gmail.com>
LicenseLGPL-3
Version1.10.0
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...

Functions

AllGeneSymbols Man page
annotationListToMatrix Man page
clEnrich Man page
clEnrich_one Man page
clusterMethods Man page
clusterMethods,cogena-method Man page
clusterMethods,cogena_methods Man page
clusterMethods,genecl-method Man page
clusterMethods,genecl_methods Man page
coExp Man page
cogean_package Man page
cogena Man page
cogena-class Man page
cogena_package Man page
cogena_package-package Man page
corInCluster Man page
corInCluster,cogena-method Man page
corInCluster,cogena_methods Man page
DEexprs Man page
enrichment Man page
enrichment,cogena-method Man page
enrichment,cogena_methods Man page
gene2set Man page
genecl-class Man page
geneclusters Man page
geneclusters,cogena-method Man page
geneclusters,cogena_methods Man page
geneclusters,genecl-method Man page
geneclusters,genecl_methods Man page
geneExpInCluster Man page
geneExpInCluster,cogena-method Man page
geneExpInCluster,cogena_methods Man page
geneInCluster Man page
geneInCluster,cogena-method Man page
geneInCluster,cogena_methods,cluster_methods Man page
gmt2list Man page
gmtlist2file Man page
heatmap.3 Man page
heatmapCluster Man page
heatmapCluster,cogena-method Man page
heatmapCmap Man page
heatmapCmap,cogena Man page
heatmapCmap,cogena-method Man page
heatmapPEI Man page
heatmapPEI,cogena Man page
heatmapPEI,cogena-method Man page
logfc Man page
logfc, Man page
mat Man page
mat,cogena-method Man page
mat,cogena_methods Man page
mat,genecl-method Man page
mat,genecl_methods Man page
nClusters Man page
nClusters,cogena-method Man page
nClusters,cogena_methods Man page
nClusters,genecl-method Man page
nClusters,genecl_methods Man page
pClusters Man page
PEI Man page
plot.sota Man page
print.sota Man page
Psoriasis Man page
Psoriasis,DEexprs,sampleLabel,cogena_result Man page
sampleLabel Man page
show,cogena-method Man page
show,cogena_methods Man page
show,genecl-method Man page
sota Man page
summary,cogena-method Man page
summary,cogena_methods Man page
summary,genecl-method Man page
upDownGene Man page
upDownGene,cogena Man page
upDownGene,cogena-method Man page

Files

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

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