Package: fenr 1.11.1

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_1.11.1.tar.gz
fenr_1.11.1.zip(r-4.7)fenr_1.11.1.zip(r-4.6)fenr_1.11.1.zip(r-4.5)
fenr_1.11.1.tgz(r-4.6-any)fenr_1.11.1.tgz(r-4.5-any)
fenr_1.11.1.tar.gz(r-4.7-any)fenr_1.11.1.tar.gz(r-4.6-any)
fenr_1.11.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fenr/json (API)

# 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-1.11.0(bioc 3.24)fenr-1.10.0(bioc 3.23)

functionalprediction differentialexpression genesetenrichment go kegg reactome proteomics

4.95 score 1 packages 8 scripts 16 exports 78 dependencies

Last updated from:892ffb428a. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	179
linux-devel-x86_64	NOTE	291
source / vignettes	OK	240
linux-release-x86_64	NOTE	344
macos-release-arm64	NOTE	316
macos-oldrel-arm64	NOTE	340
windows-devel	NOTE	324
windows-release	NOTE	237
windows-oldrel	NOTE	232
wasm-release	OK	174

Exports:enrichment_interactive fetch_bp fetch_go fetch_go_species fetch_kegg fetch_kegg_species fetch_reactome fetch_reactome_species fetch_terms_for_example fetch_wiki fetch_wiki_species functional_enrichment get_feature_terms get_term_features prepare_for_enrichment remove_cache

Dependencies:askpass assertthat base64enc BiocFileCache bit bit64 blob bslib cachem cli clipr commonmark cpp11 crayon curl DBI dbplyr digest dplyr farver fastmap filelock fontawesome fs generics ggplot2 glue gtable hms htmltools httpuv httr httr2 isoband jquerylib jsonlite labeling later lifecycle magrittr memoise mime openssl otel pillar pkgconfig prettyunits progress promises purrr R6 rappdirs RColorBrewer Rcpp readr rlang RSQLite rvest S7 sass scales selectr shiny sourcetools stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr xml2 xtable

Fast functional enrichment

Rendered fromfenr.Rmdusingknitr::rmarkdown

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

Help page	Topics
Small Shiny app serving as example for fast enrichment	enrichment_interactive
Example set of background genes.	exmpl_all
Example set of selected genes.	exmpl_sel
Get functional term data from BioPlanet	fetch_bp
Get Gene Ontology (GO) data	fetch_go
Find all species available from geneontology.org	fetch_go_species
Get functional term data from KEGG	fetch_kegg
Find all species available from KEGG	fetch_kegg_species
Get functional term data from Reactome	fetch_reactome
List of available Reactome species	fetch_reactome_species
Create term data for interactive example	fetch_terms_for_example
Get functional term data from WikiPathways	fetch_wiki
List of available WikiPathways species	fetch_wiki_species
Fast Functional Enrichment	functional_enrichment
Get terms annotating a given feature.	get_feature_terms
Get features annotated with a given term.	get_term_features
GO-terms data downloaded for the vignette.	go
GO species	go_species
Prepare Term Data for Enrichment Analysis	prepare_for_enrichment
Remove all cache	remove_cache
Differential expression results for yeast RNA-seq.	yeast_de

Package: fenr 1.11.1

fenr: Fast functional enrichment for interactive applications

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Help Manual

Usage by other packages (reverse dependencies)