Package: hypeR 2.11.1

Andrew Chen

hypeR: An R Package For Geneset Enrichment Workflows

An R Package for Geneset Enrichment Workflows.

Authors:Anthony Federico [aut], Andrew Chen [aut, cre], Stefano Monti [aut]

hypeR_2.11.1.tar.gz
hypeR_2.11.1.zip(r-4.7-any)hypeR_2.11.1.zip(r-4.6-any)hypeR_2.11.1.zip(r-4.5-any)
hypeR_2.11.1.tgz(r-4.6-any)hypeR_2.11.1.tgz(r-4.5-any)
hypeR_2.11.1.tar.gz(r-4.7-any)hypeR_2.11.1.tar.gz(r-4.6-any)
hypeR_2.11.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
hypeR/json (API)

# Install 'hypeR' in R:

install.packages('hypeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/montilab/hyper/issues

Datasets:

limma - Differential Expression
wgcna - Co-expression Modules

On BioConductor:hypeR-2.11.1(bioc 3.24)hypeR-2.10.0(bioc 3.23)

genesetenrichment annotation pathways bioinformatics computational-biology geneset-enrichment-analysis

9.18 score 79 stars 354 scripts 528 downloads 3 mentions 34 exports 90 dependencies

Last updated from:dc219ec2eb. Checks:1 WARNING, 3 ERROR, 2 OK, 4 NOTE. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	216
linux-devel	ERROR	456
source / vignettes	OK	288
linux-release	NOTE	485
macos-release	NOTE	296
macos-oldrel	ERROR	325
windows-devel	ERROR	312
windows-release	NOTE	268
windows-oldrel	NOTE	316
wasm-release	OK	132

Exports:clean_genesets enrichr_available enrichr_download enrichr_gsets genesets_Server genesets_UI ggempty ggeplot ggvenn gsets hyp hyp_dots hyp_emap hyp_hmap hyp_show hyp_to_excel hyp_to_graph hyp_to_rmd hyp_to_table hypeR hyperdb_available hyperdb_gsets hyperdb_rgsets msigdb_available msigdb_download msigdb_gsets msigdb_info msigdb_species msigdb_version multihyp rctbl_build rctbl_hyp rctbl_mhyp rgsets

Dependencies:askpass assertthat babelgene base64enc BiocManager BiocStyle bookdown bslib cachem cli commonmark cpp11 curl digest dplyr evaluate farver fastmap fontawesome fs generics ggforce ggplot2 glue gtable highr htmltools htmlwidgets httpuv httr igraph isoband jquerylib jsonlite kableExtra knitr labeling later lattice lifecycle magrittr MASS Matrix memoise mime msigdbr openssl openxlsx otel pillar pkgconfig plyr polyclip promises purrr R6 rappdirs RColorBrewer Rcpp reactable reactR reshape2 rlang rmarkdown rstudioapi S7 sass scales shiny sourcetools stringi stringr svglite sys systemfonts textshaping tibble tidyselect tinytex tweenr utf8 vctrs viridisLite visNetwork withr xfun xml2 xtable yaml zip

hypeR

Rendered fromhypeR.Rmdusingknitr::rmarkdown

Last update: 2025-06-02
Started: 2019-01-29

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Clean labels of genesets	clean_genesets
Get enrichr available genesets	enrichr_available
Download data from enrichr in the form of a named list	enrichr_download
Download data from enrichr in the form of a gsets object	enrichr_gsets
Shiny server module for geneset selection	genesets_Server
Shiny interface module for geneset selection	genesets_UI
An empty ggplot	ggempty
Enrichment plot implemented in ggplot	ggeplot
Venn diagram implemented in ggplot	ggvenn
A genesets object	gsets
A hyp object	hyp
Visualize hyp/multihyp objects as a dots plot	hyp_dots
Visualize hyp/multihyp objects as an enrichment map	hyp_emap
Visualize hyp/multihyp objects as a hiearchy map	hyp_hmap
Convert a hyp object to a reactable table	hyp_show
Export hyp/multihyp object to excel	hyp_to_excel
Convert a hyp object to an igraph object	hyp_to_graph
Export hyp object to rmarkdown	hyp_to_rmd
Export hyp/multihyp object to table	hyp_to_table
Calculate enrichment of one or more signatures	hypeR
Check available data to download from hyperdb	hyperdb_available
Download data from hyperdb	hyperdb_gsets
Download data from hyperdb in the form of a rgsets object	hyperdb_rgsets
Differential Expression	limma
Get msigdbr available genesets	msigdb_available
Download data from msigdb in the form of a named list	msigdb_download
Download data from msigdb in the form of a gsets object	msigdb_gsets
Print msigdb gsets information	msigdb_info
Get msigdbr available species	msigdb_species
Get msigdbr package version number	msigdb_version
A multihyp object	multihyp
Reactable builder for hyp or mhyp objects	rctbl_build
Reactable table for hyp objects	rctbl_hyp
Reactable table for multihyp objects	rctbl_mhyp
A relational genesets object	rgsets
Co-expression Modules	wgcna