Abstract | A quick start | Data Input | Input data required | Example dataset | Various Analyses | What kind of analysis can be done? | Types of analyses | Pathway Analysis | Parameter setting | Cogena running | Results of pathway analysis | Summary of cogena result | Heatmap of expression profiling with clusters | Enrichment heatmap of co-expressed genes | Drug repositioning | Drug repositioning analysis running | Original result of drug repositioning | Multi-instance merged result of drug repositioning | Other useful functions | Querying genes in a certain cluster | Gene expression profiling with cluster information | The gene correlation in a cluster | Bug Report | Citation | Other Information
Package: cogena 1.47.0
Zhilong Jia
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.
Authors:
cogena_1.47.0.tar.gz
cogena_1.47.0.zip(r-4.7)cogena_1.47.0.zip(r-4.6)cogena_1.47.0.zip(r-4.5)
cogena_1.47.0.tgz(r-4.6-any)cogena_1.47.0.tgz(r-4.5-any)
cogena_1.47.0.tar.gz(r-4.7-any)cogena_1.47.0.tar.gz(r-4.6-any)
cogena_1.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cogena/json (API)
| # Install 'cogena' in R: |
| install.packages('cogena', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/zhilongjia/cogena/issues
Datasets:
- AllGeneSymbols - All the gene symbols
- DEexprs - Gene expression of DEG
- sampleLabel - Label of samples
On BioConductor:cogena-1.47.0(bioc 3.24)cogena-1.46.0(bioc 3.23)
clusteringgenesetenrichmentgeneexpressionvisualizationpathwayskegggomicroarraysequencingsystemsbiologydatarepresentationdataimportbioconductorbioinformatics
Last updated from:4a6fc62eb0. Checks:8 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 191 | ||
| linux-devel-x86_64 | WARNING | 361 | ||
| source / vignettes | OK | 270 | ||
| linux-release-x86_64 | WARNING | 311 | ||
| macos-release-arm64 | WARNING | 171 | ||
| macos-oldrel-arm64 | WARNING | 156 | ||
| windows-devel | WARNING | 225 | ||
| windows-release | WARNING | 217 | ||
| windows-oldrel | WARNING | 231 | ||
| wasm-release | OK | 175 |
Exports:clEnrichclEnrich_oneclusterMethodscoExpcorInClusterenrichmentgene2setgeneclustersgeneExpInClustergeneInClustergmt2listgmtlist2fileheatmapClusterheatmapCmapheatmapPEIlogfcmatnClustersPEIshowsotasummaryupDownGene
Dependencies:amapapclusteraskpassbase64encBiobaseBiocGenericsbitopsbiwtbrewbriobslibcachemcallrcaToolsclassclicliprclustercodetoolscommonmarkcorrplotcpp11crayoncredentialscurlDEoptimRdescdevtoolsdiffobjdigestdoParalleldownlitdplyrellipsisevaluatefansifarverfastclusterfastmapfontawesomeforeachfsgenericsgertggplot2gitcredsgluegplotsgtablegtoolshighrhtmltoolshtmlwidgetshttpuvhttr2iniisobanditeratorsjquerylibjsonliteKernSmoothknitrkohonenlabelinglaterlatticelifecyclemagrittrMASSMatrixmclustmemoisemimeminiUIopensslotelpakpillarpkgbuildpkgconfigpkgdownpkgloadplyrpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrappdirsrcmdcheckRColorBrewerRcppreshape2rlangrmarkdownrobustbaseroxygen2rprojrootrstudioapirversionsS7sassscalessessioninfoshinysourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletidyrtidyselecttinytexurlcheckerusethisutf8vctrsviridisLitewaldowhiskerwithrxfunxml2xopenxtableyamlzip
a workflow of cogena
Last update: 2020-03-20
Started: 2015-10-14
cogena, a workflow for gene set enrichment analysis of co-expressed genes
Abstract | A quick start | Data Input | Input data required | Example dataset | Various Analyses | What kind of analysis can be done? | Types of analyses | Pathway Analysis | Parameter setting | Cogena running | Results of pathway analysis | Summary of cogena result | Heatmap of expression profiling with clusters | Enrichment heatmap of co-expressed genes | Drug repositioning | Drug repositioning analysis running | Original result of drug repositioning | Multi-instance merged result of drug repositioning | Other useful functions | Querying genes in a certain cluster | Gene expression profiling with cluster information | The gene correlation in a cluster | Bug Report | Citation | Other Information
Last update: 2020-03-20
Started: 2016-03-31
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| All the gene symbols | AllGeneSymbols |
| Gene set enrichment for clusters | clEnrich |
| Gene set enrichment for clusters (for one clustering method and a certain number of clusters) | clEnrich_one |
| Basic methods for a genecl object. | clusterMethods clusterMethods,cogena-method clusterMethods,cogena_methods clusterMethods,genecl-method clusterMethods,genecl_methods |
| co-expressed gene-set enrichment analysis | coExp |
| Co-expressed gene set enrichment analysis | cogean_package cogena cogena_package |
| An S4 class to represent co-expressed gene-set enrichment analysis result. | cogena-class |
| Correlation in the cluster of a cogena object | corInCluster corInCluster,cogena-method corInCluster,cogena_methods |
| gene expression of DEG | DEexprs |
| get the enrichment table from a cogena object. | enrichment enrichment,cogena-method enrichment,cogena_methods |
| generate relationship between genes and gene-sets | annotationListToMatrix gene2set |
| An S4 class to represent co-expressed gene | genecl-class |
| geneclusters: get the cluster information of a certain clustering method with a certain number. | geneclusters geneclusters,cogena-method geneclusters,cogena_methods geneclusters,genecl-method geneclusters,genecl_methods |
| Get gene names in each clusters and the expression profiling. | geneExpInCluster geneExpInCluster,cogena-method geneExpInCluster,cogena_methods |
| Get gene names in a certain cluster. | geneInCluster geneInCluster,cogena-method geneInCluster,cogena_methods,cluster_methods |
| read gmt file as a list | gmt2list |
| write gmt list into gmt file | gmtlist2file |
| heatmap of gene expression profilings with cluster indication. | heatmapCluster heatmapCluster,cogena-method |
| heatmap designed for for CMap gene set only | heatmapCmap heatmapCmap,cogena heatmapCmap,cogena-method |
| heatmap of the gene set enrichment from a cogena object. | heatmapPEI heatmapPEI,cogena heatmapPEI,cogena-method |
| mat: get the original data from a genecl object. | mat mat,cogena-method mat,cogena_methods mat,genecl-method mat,genecl_methods |
| nClusters: get the number of clusters from a genecl object. | nClusters nClusters,cogena-method nClusters,cogena_methods nClusters,genecl-method nClusters,genecl_methods |
| Significance of Gene sets enrichment. | PEI |
| Psoriasis dataset. | Psoriasis Psoriasis,DEexprs,sampleLabel,cogena_result |
| label of samples | sampleLabel |
| show: show the class of cogena or genecl object | show,cogena-method show,cogena_methods show,genecl-method |
| Self-organizing tree algorithm (SOTA) | plot.sota print.sota sota |
| summary: a summary of a genecl object. | summary,cogena-method summary,cogena_methods summary,genecl-method |
| Show up or down-regualted genes for a clustering method and the number of clusters. | logfc logfc, upDownGene upDownGene,cogena upDownGene,cogena-method |
