Package: fenr 1.5.0

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_1.5.0.tar.gz
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fenr_1.5.0.tgz(r-4.4-any)fenr_1.5.0.tgz(r-4.3-any)
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fenr_1.5.0.tgz(r-4.4-emscripten)fenr_1.5.0.tgz(r-4.3-emscripten)
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-1.5.0(bioc 3.21)fenr-1.4.0(bioc 3.20)

functionalpredictiondifferentialexpressiongenesetenrichmentgokeggreactomeproteomics

4.70 score 3 scripts 144 downloads 16 exports 85 dependencies

Last updated 2 months agofrom:56741379e7. Checks:OK: 5 ERROR: 2. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 10 2024
R-4.5-winOKDec 10 2024
R-4.5-linuxOKDec 10 2024
R-4.4-winOKDec 10 2024
R-4.4-macERRORDec 10 2024
R-4.3-winOKDec 10 2024
R-4.3-macERRORDec 10 2024

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 Dec 10 2024.

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