Man pages for hypeR
An R Package For Geneset Enrichment Workflows
| clean_genesets | Clean labels of genesets |
| dot-check_overlap | Check overlap of signature across genesets |
| dot-dots_multi_plot | Plot top enriched genesets across multiple signatures |
| dot-dots_plot | Plot top enriched genesets |
| dot-enrichment_map | Plot enrichment map |
| dot-find_members | Find geneset members |
| dot-format_str | Format a string using placeholders |
| dot-hiearchy_map | Plot hiearchy map |
| dot-hyper_enrichment | Overrepresentation test via hyper-geometric distribution |
| dot-jaccard_similarity | Calculate jaccard similarity of two sets |
| dot-ks_enrichment | Enrichment test via one-sided Kolmogorov<e2><80><93>Smirnov... |
| dot-kstest | One-sided Kolmogorov<e2><80><93>Smirnov test |
| dot-overlap_similarity | Calculate overlap similarity of two sets |
| dot-reverselog_trans | Custom reverse log transformation of continous ggplot axes |
| dot-string_args | Convert an arguments list to string format |
| enrichr_available | Get enrichr available genesets |
| enrichr_connect | Connect to the enrichr web application |
| enrichr_download | Download data from enrichr in the form of a named list |
| enrichr_gsets | Download data from enrichr in the form of a gsets object |
| enrichr_urls | Get url base for species-specific enrichr libraries |
| genesets_Server | Shiny server module for geneset selection |
| genesets_UI | Shiny interface module for geneset selection |
| ggempty | An empty ggplot |
| ggeplot | Enrichment plot implemented in ggplot |
| ggvenn | Venn diagram implemented in ggplot |
| gsets | A genesets object |
| hyp | A hyp object |
| hyp_dots | Visualize hyp/multihyp objects as a dots plot |
| hyp_emap | Visualize hyp/multihyp objects as an enrichment map |
| hypeR | Calculate enrichment of one or more signatures |
| hyperdb_info | Print hypeR-db rgsets information |
| hyperdb_rgsets | Download data from hyperdb in the form of a rgsets object |
| hyp_hmap | Visualize hyp/multihyp objects as a hiearchy map |
| hyp_show | Convert a hyp object to a reactable table |
| hyp_to_excel | Export hyp/multihyp object to excel |
| hyp_to_rmd | Export hyp object to rmarkdown |
| hyp_to_table | Export hyp/multihyp object to table |
| limma | Differential Expression |
| msigdb_available | Get msigdbr available genesets |
| msigdb_check_species | Check if species is available |
| msigdb_download | Download data from msigdb in the form of a named list |
| msigdb_gsets | Download data from msigdb in the form of a gsets object |
| msigdb_info | Print msigdb gsets information |
| msigdb_species | Get msigdbr available species |
| msigdb_version | Get msigdbr package version number |
| multihyp | A multihyp object |
| pvector | A push/pop capable vector |
| rctbl_build | Reactable builder for hyp or mhyp objects |
| rctbl_hyp | Reactable table for hyp objects |
| rctbl_mhyp | Reactable table for multihyp objects |
| rgsets | A relational genesets object |
| wgcna | Co-expression Modules |
