├── .Rbuildignore ├── .github └── issue_template.md ├── .gitignore ├── CONTRIBUTING.md ├── DESCRIPTION ├── Makefile ├── NAMESPACE ├── NEWS ├── NEWS.md ├── R ├── 00-AllClasses.R ├── AllGenerics.R ├── GFFparser.R ├── accessor.R ├── bitr.R ├── clusterProfiler-package.R ├── compareCluster.R ├── data.R ├── dplyr-arrange.R ├── dplyr-filter.R ├── dplyr-group_by.R ├── dplyr-mutate.R ├── dplyr-rename.R ├── dplyr-select.R ├── dplyr-slice.R ├── dplyr-summarise.R ├── enrichDAVID.R ├── enrichGO.R ├── enrichKEGG.R ├── enrichMKEGG.R ├── enricher.R ├── enrichit.R ├── enrichplot.R ├── go-utilities.R ├── gofilter.R ├── groupGO.R ├── gseAnalyzer.R ├── gson.R ├── kegg-utilities.R ├── pathwayCommons.R ├── plotGOgraph.R ├── ppi.R ├── reexports.R ├── simplify.R ├── taxa.R ├── uniprot.R ├── utilities.R ├── wikiPathways.R └── zzz.R ├── README.Rmd ├── README.md ├── data ├── DE_GSE8057.rda ├── gcSample.rda ├── kegg_category.rda └── kegg_species.rda ├── docs └── index.html ├── graphic-abstract-The-Innovation-2021.jpg ├── inst ├── CITATION └── extdata │ ├── c5.cc.v5.0.entrez.gmt │ ├── kegg-mapper-blast.txt │ ├── kegg_pathway_category.r │ ├── kegg_taxa.rds │ └── wikipathways-20180810-gmt-Homo_sapiens.gmt ├── man ├── DataSet.Rd ├── GSEA.Rd ├── Gff2GeneTable.Rd ├── append_kegg_category.Rd ├── bitr.Rd ├── bitr_kegg.Rd ├── browseKEGG.Rd ├── clusterProfiler-package.Rd ├── compareCluster.Rd ├── download_KEGG.Rd ├── dropGO.Rd ├── enrichDAVID.Rd ├── enrichGO.Rd ├── enrichKEGG.Rd ├── enrichMKEGG.Rd ├── enrichPC.Rd ├── enrichWP.Rd ├── enricher.Rd ├── getPPI.Rd ├── getTaxID.Rd ├── getTaxInfo.Rd ├── get_wp_organisms.Rd ├── go2ont.Rd ├── go2term.Rd ├── gofilter.Rd ├── groupGO.Rd ├── groupGOResult-class.Rd ├── gseGO.Rd ├── gseKEGG.Rd ├── gseMKEGG.Rd ├── gsePC.Rd ├── gseWP.Rd ├── gson_GO.Rd ├── gson_KEGG.Rd ├── gson_KEGG_mapper.Rd ├── gson_WP.Rd ├── idType.Rd ├── ko2name.Rd ├── merge_result.Rd ├── plotGOgraph.Rd ├── read.gmt.pc.Rd ├── reexports.Rd ├── search_kegg_organism.Rd 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