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| clusterProfiler-package | statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters. |
| bitr | bitr |
| bitr_kegg | bitr_kegg |
| browseKEGG | browseKEGG |
| buildGOmap | buildGOmap |
| clusterProfiler | statistical analysis and visualization of functional profiles for genes and gene clusters The package implements methods to analyze and visualize functional profiles of gene and gene clusters. |
| compareCluster | Compare gene clusters functional profile |
| compareClusterResult-class | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis. |
| DataSet | Datasets gcSample contains a sample of gene clusters. |
| dotplot-method | dotplot |
| download_KEGG | download_KEGG |
| dropGO | dropGO |
| enrichDAVID | enrichDAVID |
| enricher | enricher |
| enrichGO | GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control. |
| enrichKEGG | KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control. |
| enrichMKEGG | KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control. |
| fortify.compareClusterResult | fortify |
| gcSample | Datasets gcSample contains a sample of gene clusters. |
| getGOLevel | get GOIDs at a specific level |
| Gff2GeneTable | Gff2GeneTable |
| go2ont | go2ont |
| go2term | go2term |
| gofilter | gofilter |
| groupGO | Functional Profile of a gene set at specific GO level. Given a vector of genes, this function will return the GO profile at a specific level. |
| groupGOResult-class | Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level. |
| GSEA | GSEA |
| gseGO | gseGO |
| gseKEGG | gseKEGG |
| gseMKEGG | gseMKEGG |
| idType | idType |
| KEGG_path2extid | KEGG_path2extid |
| kegg_species | Datasets gcSample contains a sample of gene clusters. |
| ko2name | ko2name |
| merge_result | merge_result |
| plot-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis. |
| plotGOgraph | plotGOgraph |
| plotting.clusterProfile | plotting-clusterProfile |
| read.gmt | read.gmt |
| search_kegg_organism | search_kegg_organism |
| show-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis. |
| show-method | Class "groupGOResult" This class represents the result of functional Profiles of a set of gene at specific GO level. |
| simplify | simplify method |
| simplify-method | simplify method |
| summary-method | Class "compareClusterResult" This class represents the comparison result of gene clusters by GO categories at specific level or GO enrichment analysis. |
| uniprot_get | uniprot_get |
| viewKEGG | viewKEGG function is for visualize KEGG pathways works with enrichResult object to visualize enriched KEGG pathway |