Package: fenr 1.5.2

Marek Gierlinski

fenr: Fast functional enrichment for interactive applications

Perform fast functional enrichment on feature lists (like genes or proteins) using the hypergeometric distribution. Tailored for speed, this package is ideal for interactive platforms such as Shiny. It supports the retrieval of functional data from sources like GO, KEGG, Reactome, Bioplanet and WikiPathways. By downloading and preparing data first, it allows for rapid successive tests on various feature selections without the need for repetitive, time-consuming preparatory steps typical of other packages.

Authors:Marek Gierlinski [aut, cre]

fenr_1.5.2.tar.gz
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fenr.pdf |fenr.html✨
fenr/json (API)
NEWS

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

Bug tracker:https://github.com/bartongroup/fenr/issues

Datasets:
  • exmpl_all - Example set of background genes.
  • exmpl_sel - Example set of selected genes.
  • go - GO-terms data downloaded for the vignette.
  • go_species - GO species
  • yeast_de - Differential expression results for yeast RNA-seq.

On BioConductor:fenr-1.5.1(bioc 3.21)fenr-1.4.1(bioc 3.20)

functionalpredictiondifferentialexpressiongenesetenrichmentgokeggreactomeproteomics

4.60 score 4 scripts 186 downloads 16 exports 85 dependencies

Last updated 2 days agofrom:e0fb64240c. Checks:8 OK. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 21 2025
R-4.5-winOKFeb 21 2025
R-4.5-macOKFeb 21 2025
R-4.5-linuxOKFeb 21 2025
R-4.4-winOKFeb 21 2025
R-4.4-macOKFeb 21 2025
R-4.3-winOKFeb 21 2025
R-4.3-macOKFeb 21 2025

Exports:enrichment_interactivefetch_bpfetch_gofetch_go_speciesfetch_keggfetch_kegg_speciesfetch_reactomefetch_reactome_speciesfetch_terms_for_examplefetch_wikifetch_wiki_speciesfunctional_enrichmentget_feature_termsget_term_featuresprepare_for_enrichmentremove_cache

Dependencies:askpassassertthatbase64encBiocFileCachebitbit64blobbslibcachemclicliprcolorspacecommonmarkcpp11crayoncurlDBIdbplyrdigestdplyrfansifarverfastmapfilelockfontawesomefsgenericsggplot2gluegtablehmshtmltoolshttpuvhttrhttr2isobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpillarpkgconfigplogrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppreadrrlangRSQLitervestsassscalesselectrshinysourcetoolsstringistringrsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithrxml2xtable

Fast functional enrichment

Marek Gierlinski

Rendered fromfenr.Rmdusingknitr::rmarkdownon Feb 21 2025.

Last update: 2025-02-20
Started: 2022-08-22