{ "_id": "6a1adaca1d7bb097a09e8afc", "Package": "cogena", "Version": "1.47.0", "Title": "co-expressed gene-set enrichment analysis", "Authors@R": "c(person(\"Zhilong\", \"Jia\", role =c(\"aut\", \"cre\"), \nemail=\"zhilongjia@gmail.com\"),\nperson(\"Michael\", \"Barnes\", role = \"aut\", email=\"m.r.barnes@qmul.ac.uk\"))", "Description": "cogena is a workflow for co-expressed gene-set enrichment\nanalysis. It aims to discovery smaller scale, but highly\ncorrelated cellular events that may be of great biological\nrelevance. A novel pipeline for drug discovery and drug\nrepositioning based on the cogena workflow is proposed.\nParticularly, candidate drugs can be predicted based on the\ngene expression of disease-related data, or other similar drugs\ncan be identified based on the gene expression of drug-related\ndata. Moreover, the drug mode of action can be disclosed by the\nassociated pathway analysis. In summary, cogena is a flexible\nworkflow for various gene set enrichment analysis for\nco-expressed genes, with a focus on pathway/GO analysis and\ndrug repositioning.", "biocViews": "Clustering, GeneSetEnrichment, GeneExpression,\nVisualization, Pathways, KEGG, GO, Microarray, Sequencing,\nSystemsBiology, DataRepresentation, DataImport", "Collate": "dist_class.R genecl_class.R cogena_class.R Class_methods.R\ncogena.R upDownGene.R PEI.R sota.R pClusters.R coExp.R\nclEnrich.R clEnrich_one.R enrichment.R gene2set.R\ngeneInCluster.R geneExpInCluster.R corInCluster.R gmt2list.R\ngmtlist2file.R heatmap.3.R heatmapCluster.R heatmapPEI.R\nheatmapCmap.R", "License": "LGPL-3", "LazyData": "true", "Encoding": "UTF-8", "URL": "https://github.com/zhilongjia/cogena", "NeedsCompilation": "no", "BugReports": "https://github.com/zhilongjia/cogena/issues", "VignetteBuilder": "knitr", "RoxygenNote": "7.0.2", "Config/pak/sysreqs": "cmake libfontconfig1-dev libfreetype6-dev\nlibfribidi-dev git make 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