Package: hypeR 2.5.0

Anthony Federico

hypeR: An R Package For Geneset Enrichment Workflows

An R Package for Geneset Enrichment Workflows.

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

hypeR_2.5.0.tar.gz
hypeR_2.5.0.zip(r-4.5)hypeR_2.5.0.zip(r-4.4)hypeR_2.5.0.zip(r-4.3)
hypeR_2.5.0.tgz(r-4.4-any)hypeR_2.5.0.tgz(r-4.3-any)
hypeR_2.5.0.tar.gz(r-4.5-noble)hypeR_2.5.0.tar.gz(r-4.4-noble)
hypeR_2.5.0.tgz(r-4.4-emscripten)hypeR_2.5.0.tgz(r-4.3-emscripten)
hypeR.pdf |hypeR.html✨
hypeR/json (API)
NEWS

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

Peer review:

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

On BioConductor:hypeR-2.3.0(bioc 3.20)hypeR-2.2.0(bioc 3.19)

genesetenrichmentannotationpathwaysbioinformaticscomputational-biologygeneset-enrichment-analysis

8.19 score 76 stars 135 scripts 218 downloads 3 mentions 34 exports 93 dependencies

Last updated 25 days agofrom:2152271546. Checks:OK: 1 WARNING: 4 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winWARNINGOct 30 2024
R-4.5-linuxWARNINGOct 30 2024
R-4.4-winWARNINGOct 30 2024
R-4.4-macERROROct 30 2024
R-4.3-winWARNINGOct 30 2024
R-4.3-macERROROct 30 2024

Exports:clean_genesetsenrichr_availableenrichr_downloadenrichr_gsetsgenesets_Servergenesets_UIggemptyggeplotggvenngsetshyphyp_dotshyp_emaphyp_hmaphyp_showhyp_to_excelhyp_to_graphhyp_to_rmdhyp_to_tablehypeRhyperdb_availablehyperdb_gsetshyperdb_rgsetsmsigdb_availablemsigdb_downloadmsigdb_gsetsmsigdb_infomsigdb_speciesmsigdb_versionmultihyprctbl_buildrctbl_hyprctbl_mhyprgsets

Dependencies:askpassbabelgenebase64encBiocManagerBiocStylebookdownbslibcachemclicolorspacecommonmarkcpp11crayoncurldigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggforceggplot2gluegtablehighrhtmltoolshtmlwidgetshttpuvhttrigraphisobandjquerylibjsonlitekableExtraknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemsigdbrmunsellnlmeopensslopenxlsxpillarpkgconfigplyrpolyclippromisespurrrR6rappdirsRColorBrewerRcppRcppEigenreactablereactRreshape2rlangrmarkdownrstudioapisassscalesshinysourcetoolsstringistringrsvglitesyssystemfontstibbletidyselecttinytextweenrutf8vctrsviridisLitevisNetworkwithrxfunxml2xtableyamlzip

hypeR

Anthony Federico, Stefano Monti

Rendered fromhypeR.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2021-07-01
Started: 2019-01-29

Readme and manuals

Help Manual

Help pageTopics
Clean labels of genesetsclean_genesets
Get enrichr available genesetsenrichr_available
Download data from enrichr in the form of a named listenrichr_download
Download data from enrichr in the form of a gsets objectenrichr_gsets
Shiny server module for geneset selectiongenesets_Server
Shiny interface module for geneset selectiongenesets_UI
An empty ggplotggempty
Enrichment plot implemented in ggplotggeplot
Venn diagram implemented in ggplotggvenn
A genesets objectgsets
A hyp objecthyp
Visualize hyp/multihyp objects as a dots plothyp_dots
Visualize hyp/multihyp objects as an enrichment maphyp_emap
Visualize hyp/multihyp objects as a hiearchy maphyp_hmap
Convert a hyp object to a reactable tablehyp_show
Export hyp/multihyp object to excelhyp_to_excel
Convert a hyp object to an igraph objecthyp_to_graph
Export hyp object to rmarkdownhyp_to_rmd
Export hyp/multihyp object to tablehyp_to_table
Calculate enrichment of one or more signatureshypeR
Check available data to download from hyperdbhyperdb_available
Download data from hyperdbhyperdb_gsets
Download data from hyperdb in the form of a rgsets objecthyperdb_rgsets
Differential Expressionlimma
Get msigdbr available genesetsmsigdb_available
Download data from msigdb in the form of a named listmsigdb_download
Download data from msigdb in the form of a gsets objectmsigdb_gsets
Print msigdb gsets informationmsigdb_info
Get msigdbr available speciesmsigdb_species
Get msigdbr package version numbermsigdb_version
A multihyp objectmultihyp
Reactable builder for hyp or mhyp objectsrctbl_build
Reactable table for hyp objectsrctbl_hyp
Reactable table for multihyp objectsrctbl_mhyp
A relational genesets objectrgsets
Co-expression Moduleswgcna