Man pages for hypeR
An R Package For Geneset Enrichment Workflows

clean_genesetsClean labels of genesets
dot-check_overlapCheck overlap of signature across genesets
dot-dots_multi_plotPlot top enriched genesets across multiple signatures
dot-dots_plotPlot top enriched genesets
dot-enrichment_mapPlot enrichment map
dot-find_membersFind geneset members
dot-format_strFormat a string using placeholders
dot-hiearchy_mapPlot hiearchy map
dot-hyper_enrichmentOverrepresentation test via hyper-geometric distribution
dot-jaccard_similarityCalculate jaccard similarity of two sets
dot-ks_enrichmentEnrichment test via one-sided Kolmogorov<e2><80><93>Smirnov...
dot-kstestOne-sided Kolmogorov<e2><80><93>Smirnov test
dot-overlap_similarityCalculate overlap similarity of two sets
dot-reverselog_transCustom reverse log transformation of continous ggplot axes
dot-string_argsConvert an arguments list to string format
enrichr_availableGet enrichr available genesets
enrichr_connectConnect to the enrichr web application
enrichr_downloadDownload data from enrichr in the form of a named list
enrichr_gsetsDownload data from enrichr in the form of a gsets object
enrichr_urlsGet url base for species-specific enrichr libraries
genesets_ServerShiny server module for geneset selection
genesets_UIShiny interface module for geneset selection
ggemptyAn empty ggplot
ggeplotEnrichment plot implemented in ggplot
ggvennVenn diagram implemented in ggplot
gsetsA genesets object
hypA hyp object
hyp_dotsVisualize hyp/multihyp objects as a dots plot
hyp_emapVisualize hyp/multihyp objects as an enrichment map
hypeRCalculate enrichment of one or more signatures
hyperdb_infoPrint hypeR-db rgsets information
hyperdb_rgsetsDownload data from hyperdb in the form of a rgsets object
hyp_hmapVisualize hyp/multihyp objects as a hiearchy map
hyp_showConvert a hyp object to a reactable table
hyp_to_excelExport hyp/multihyp object to excel
hyp_to_rmdExport hyp object to rmarkdown
hyp_to_tableExport hyp/multihyp object to table
limmaDifferential Expression
msigdb_availableGet msigdbr available genesets
msigdb_check_speciesCheck if species is available
msigdb_downloadDownload data from msigdb in the form of a named list
msigdb_gsetsDownload data from msigdb in the form of a gsets object
msigdb_infoPrint msigdb gsets information
msigdb_speciesGet msigdbr available species
msigdb_versionGet msigdbr package version number
multihypA multihyp object
pvectorA push/pop capable vector
rctbl_buildReactable builder for hyp or mhyp objects
rctbl_hypReactable table for hyp objects
rctbl_mhypReactable table for multihyp objects
rgsetsA relational genesets object
wgcnaCo-expression Modules
hypeR documentation built on Nov. 8, 2020, 8:19 p.m.