Package: fedup 1.20.0

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_1.20.0.tar.gz
fedup_1.20.0.zip(r-4.7-any)fedup_1.20.0.zip(r-4.6-any)fedup_1.20.0.zip(r-4.5-any)
fedup_1.20.0.tgz(r-4.6-any)fedup_1.20.0.tgz(r-4.5-any)
fedup_1.20.0.tar.gz(r-4.7-any)fedup_1.20.0.tar.gz(r-4.6-any)
fedup_1.20.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fedup/json (API)

# Install 'fedup' in R:
install.packages('fedup', repos = c('https://bioc-release.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

5.56 score 8 stars 15 scripts 442 downloads 7 exports 65 dependencies

Last updated from:240819c1eb (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING168
linux-develNOTE370
source / vignettesOK285
linux-releaseNOTE379
macos-releaseNOTE273
macos-oldrelNOTE168
windows-develNOTE228
windows-releaseNOTE228
windows-oldrelNOTE203
wasm-releaseOK139

Exports:plotDotPlotplotFemapprepInputreadPathwaysrunFedupwriteFemapwritePathways

Dependencies:askpassbackportsbase64encbase64urlBiocGenericsbitopscaToolsclicpp11crayoncurldata.tabledigestdplyrevaluatefarverfastmapforcatsfsgenericsggplot2ggthemesgluegplotsgraphgtablegtoolshtmltoolshttrIRdisplayIRkernelisobandjsonliteKernSmoothlabelinglifecyclemagrittrmimeopensslopenxlsxpbdZMQpillarpkgconfigpurrrR6RColorBrewerRcppRCurlRCy3reprRJSONIOrlangS7scalesstringisystibbletidyselectutf8uuidvctrsviridisLitewithrXMLzip

Running fedup with a single test set
System prerequisites | Installation | Running the package | Input data | Pathway analysis | Dot plot | Enrichment map | Session information
Rendered fromfedup_singleTest.rmdusingknitr::rmarkdown

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

Running fedup with multiple test sets
System prerequisites | Installation | Running the package | Input data | Pathway analysis | Dot plot | Enrichment map | Session information
Rendered fromfedup_mutliTest.rmdusingknitr::rmarkdown

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

Running fedup with two test sets
System prerequisites | Installation | Running the package | Input data | Pathway analysis | Dot plot | Enrichment map | Session information
Rendered fromfedup_doubleTest.rmdusingknitr::rmarkdown

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