Package: fenr 1.3.1

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_1.3.1.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'))

Peer review:

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-1.3.0(bioc 3.20)fenr-1.2.0(bioc 3.19)

bioconductor-package

16 exports 1.51 score 85 dependencies

Last updated 26 days agofrom:7a2efa8f97

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 Jun 15 2024.

Last update: 2024-04-26
Started: 2022-08-22