Man pages for hurlab/RichR
Function Enrichment analysis and Network construction
| Annot-class | Class "Annot" This class represents the Annotation... |
| buildAnnot-methods | make annotation database |
| buildMSIGDB | Download database from Msigdb and prepare for enrichment... |
| buildOwn | make annotation database using bioAnno results |
| comparedot | draw dotplot for multiple enrichment results |
| compareGSEA | compare GSEA enrichment results across different samples and... |
| compareResult | compare enrichment results across different samples |
| detail | detail generic |
| detail.GSEAResult | extract the gene information and related pathway |
| detail.richResult | extract the gene information and related pathway |
| dot-calculate_Enrichment_Score | calculate enrichment score |
| dot-clean.char | remove the newlines |
| dot-getmsig | msigdb support species |
| dot-kappa | kappa function |
| dot-kappa_cluster_internal | calculate kappa cluster |
| dot-makeGOdata | make GO annotation data function |
| dot-makeKOdata | make KEGG annotation data function |
| dot-makeKOMdata | make KEGG module annotation data function |
| dot-makeROdata | make Reactome annotation data function |
| dot-merge_term | merge term |
| dot-paste.char | replace the term string with newlines |
| enrich-ANY-Annot-method | Enrichment analysis function |
| enrich-ANY-data.frame-method | Enrichment analysis function |
| enrich_internal | Enrichment analysis for any type of annotation data |
| enrich-methods | enrich method |
| getann | build annotaion for kegg |
| getdetail | get detail and integrate with the input gene information |
| ggbar | barplot for Enrichment results |
| ggbar-methods | ggbar method |
| ggdot | dotplot for Enrichment results |
| ggdot_internal | Dotplot for enrichment results |
| ggdot-methods | ggdot method |
| ggGSEA | plot the gsea result |
| ggheatmap | Plot compare heatmap of Enrichment result among DEG groups |
| ggnetmap | generate network based on Enrichment results |
| ggnetplot | richplot for Enrichment result |
| ggnetplot-method | ggnetplot method |
| ggnetplot-richResult-method | richplot for Enrichment results |
| ggnetwork | generate network based on Enrichment results |
| ggnetwork-methods | ggnetwork method |
| ggrich_internal | richplot |
| GO_child | Get all children terms of node |
| GSEAResult-class | Class "GSEAResult" This class represents the result from GSEA... |
| idconvert | Convert ID between ENTREZID to SYMBOL or other type ID based... |
| msigdbinfo | Print MSIGDB infomation |
| msigdbr | Download database from Msigdb and prepare for enrichment... |
| overlap | ovelap |
| plotGSEA | plot multiple significant pathways |
| rbind.GSEAResult | rbind generic function for GSEAResult object |
| rbind.richResult | rbind generic function for richResult object |
| reexports | Objects exported from other packages |
| result | result generic |
| reverseList | reverse List |
| richCluster | kappa cluster analysis |
| richCluster-data.frame-method | kappa cluster analysis |
| richCluster-richResult-method | kappa cluster analysis |
| richDAVID | Functional enrichment analysis with DAVID |
| richGO-ANY-Annot-method | GO Enrichment analysis function |
| richGO-ANY-data.frame-method | GO Enrichment analysis function |
| richGO_internal | GO Enrichment analysis function |
| richGO-methods | richGO method |
| richGSEA-ANY-Annot-method | GSEA Enrichment analysis function |
| richGSEA-ANY-data.frame-method | GSEA Enrichment analysis function |
| richGSEA_internal | Enrichment analysis for any type of annotation data |
| richGSEA-methods | richGSEA method |
| richKEGG-ANY-Annot-method | KEGG Enrichment analysis function |
| richKEGG-ANY-data.frame-method | KEGG Pathway Enrichment analysis function |
| richKEGG_internal | KEGG Pathway Enrichment analysis function |
| richKEGG-methods | richKEGG method |
| richLevel-ANY-Annot-method | Pathway Enrichment analysis for different level function |
| richLevel-ANY-data.frame-method | Pathway Enrichment analysis for different level function |
| richLevel_internal | Pathway Enrichment analysis for different level function |
| richLevel-methods | richLevel method |
| richResult-class | Class "richResult" This class represents the result of... |
| showData | show avaliable data based on bioconductor annotation package |
| vec_to_df | vector to data.frame |
