An R Package For Geneset Enrichment Workflows

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Documentation for package ‘hypeR’ version 2.5.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

clean_genesets	Clean labels of genesets
enrichr_available	Get enrichr available genesets
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
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
hypeR	Calculate enrichment of one or more signatures
hyperdb_available	Check available data to download from hyperdb
hyperdb_gsets	Download data from hyperdb
hyperdb_rgsets	Download data from hyperdb in the form of a rgsets object
hyp_dots	Visualize hyp/multihyp objects as a dots plot
hyp_emap	Visualize hyp/multihyp objects as an enrichment map
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_graph	Convert a hyp object to an igraph object
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_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
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