Package: fedup 1.21.0

Catherine Ross

fedup: Fisher's Test for Enrichment and Depletion of User-Defined Pathways

An R package that tests for enrichment and depletion of user-defined pathways using a Fisher's exact test. The method is designed for versatile pathway annotation formats (eg. gmt, txt, xlsx) to allow the user to run pathway analysis on custom annotations. This package is also integrated with Cytoscape to provide network-based pathway visualization that enhances the interpretability of the results.

Authors:Catherine Ross [aut, cre]

fedup_1.21.0.tar.gz
fedup_1.21.0.zip(r-4.7)fedup_1.21.0.zip(r-4.6)fedup_1.21.0.zip(r-4.5)
fedup_1.21.0.tgz(r-4.6-any)fedup_1.21.0.tgz(r-4.5-any)
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fedup_1.21.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
fedup/json (API)
NEWS

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

Bug tracker:https://github.com/rosscm/fedup/issues

Datasets:
  • geneDouble - Example list of a background set and two sets of test genes to use for enrichment analysis.
  • geneMulti - Example list of a background set and multiple sets of test genes to use for enrichment analysis.
  • geneSingle - Example list of a background set and single set of test genes to use for enrichment analysis.
  • pathwaysGMT - Named list of human pathway annotations obtained from a GMT file.
  • pathwaysTXT - Example list of SAFE terms obtained from a TXT file.
  • pathwaysXLSX - Example list of SAFE terms obtained from a XLSX file.

On BioConductor:fedup-1.21.0(bioc 3.24)fedup-1.19.0(bioc 3.23)

genesetenrichmentpathwaysnetworkenrichmentnetworkbioconductorenrichment

5.62 score 7 stars 20 scripts 338 downloads 7 exports 66 dependencies

Last updated from:816d977811. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksWARNING210
linux-devel-x86_64NOTE323
source / vignettesOK265
linux-release-x86_64NOTE348
macos-release-arm64NOTE210
macos-oldrel-arm64NOTE189
windows-develNOTE291
windows-releaseNOTE216
windows-oldrelNOTE223
wasm-releaseOK148

Exports:plotDotPlotplotFemapprepInputreadPathwaysrunFedupwriteFemapwritePathways

Dependencies:askpassbackportsbase64encbase64urlBiocGenericsbitopscaToolsclicpp11crayoncurldata.tabledigestdplyrevaluatefarverfastmapforcatsfsgenericsggplot2ggthemesgluegplotsgraphgtablegtoolshtmltoolshttrIRdisplayIRkernelisobandjsonliteKernSmoothlabelinglifecyclemagrittrmimeopensslopenxlsxpbdZMQpillarpkgconfigpurrrR6RColorBrewerRcppRCurlRCy3reprRJSONIOrlangS7scalesstringistringrsystibbletidyselectutf8uuidvctrsviridisLitewithrXMLzip

Running fedup with a single test set

Catherine Ross

Rendered fromfedup_singleTest.rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-04-24
Started: 2021-03-24

Running fedup with multiple test sets

Catherine Ross

Rendered fromfedup_mutliTest.rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-04-24
Started: 2021-03-24

Running fedup with two test sets

Catherine Ross

Rendered fromfedup_doubleTest.rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2021-04-24
Started: 2021-03-24