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'))

Peer review:

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-1.13.0(bioc 3.20)fedup-1.12.0(bioc 3.19)

genesetenrichmentpathwaysnetworkenrichmentnetworkbioconductorenrichment

5.32 score 7 stars 10 scripts 137 downloads 7 exports 72 dependencies

Last updated 23 days agofrom:6f5f84fcbb. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winOKOct 30 2024
R-4.3-macOKOct 30 2024

Exports:plotDotPlotplotFemapprepInputreadPathwaysrunFedupwriteFemapwritePathways

Dependencies:askpassbackportsbase64encbase64urlBiocGenericsbitopscaToolsclicolorspacecrayoncurldata.tabledigestdplyrevaluatefansifarverfastmapforcatsfsgenericsggplot2ggthemesgluegplotsgraphgtablegtoolshtmltoolshttrIRdisplayIRkernelisobandjsonliteKernSmoothlabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslopenxlsxpbdZMQpillarpkgconfigpurrrR6RColorBrewerRcppRCurlRCy3reprRJSONIOrlangscalesstringistringrsystibbletidyselectutf8uuidvctrsviridisLitewithrXMLzip

Running fedup with a single test set

Catherine Ross

Rendered fromfedup_singleTest.rmdusingknitr::rmarkdownon Oct 30 2024.

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

Running fedup with multiple test sets

Catherine Ross

Rendered fromfedup_mutliTest.rmdusingknitr::rmarkdownon Oct 30 2024.

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

Running fedup with two test sets

Catherine Ross

Rendered fromfedup_doubleTest.rmdusingknitr::rmarkdownon Oct 30 2024.

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