Package: fedup 1.15.0

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]

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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-1.15.0(bioc 3.21)fedup-1.14.0(bioc 3.20)

genesetenrichmentpathwaysnetworkenrichmentnetworkbioconductorenrichment

5.32 score 7 stars 10 scripts 186 downloads 7 exports 72 dependencies

Last updated 4 months agofrom:6f5f84fcbb. Checks:3 OK, 5 NOTE. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKJan 26 2025
R-4.5-winNOTEJan 26 2025
R-4.5-macNOTEJan 26 2025
R-4.5-linuxNOTEJan 26 2025
R-4.4-winNOTEJan 26 2025
R-4.4-macNOTEJan 26 2025
R-4.3-winOKJan 26 2025
R-4.3-macOKJan 26 2025

Exports:plotDotPlotplotFemapprepInputreadPathwaysrunFedupwriteFemapwritePathways

Dependencies:askpassbackportsbase64encbase64urlBiocGenericsbitopscaToolsclicolorspacecrayoncurldata.tabledigestdplyrevaluatefansifarverfastmapforcatsfsgenericsggplot2ggthemesgluegplotsgraphgtablegtoolshtmltoolshttrIRdisplayIRkernelisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslopenxlsxpbdZMQpillarpkgconfigpurrrR6RColorBrewerRcppRCurlRCy3reprRJSONIOrlangscalesstringistringrsystibbletidyselectutf8uuidvctrsviridisLitewithrXMLzip

Running fedup with a single test set

Catherine Ross

Rendered fromfedup_singleTest.rmdusingknitr::rmarkdownon Jan 26 2025.

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

Running fedup with multiple test sets

Catherine Ross

Rendered fromfedup_mutliTest.rmdusingknitr::rmarkdownon Jan 26 2025.

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

Running fedup with two test sets

Catherine Ross

Rendered fromfedup_doubleTest.rmdusingknitr::rmarkdownon Jan 26 2025.

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