Package: FGNet 3.46.0
Sara Aibar
FGNet: Functional Gene Networks derived from biological enrichment analyses
Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO.
Authors:
FGNet_3.46.0.tar.gz
FGNet_3.46.0.zip(r-4.7)FGNet_3.46.0.zip(r-4.6)FGNet_3.46.0.zip(r-4.5)
FGNet_3.46.0.tgz(r-4.6-any)FGNet_3.46.0.tgz(r-4.5-any)
FGNet_3.46.0.tar.gz(r-4.7-any)FGNet_3.46.0.tar.gz(r-4.6-any)
FGNet_3.46.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
FGNet/json (API)
NEWS
| # Install 'FGNet' in R: |
| install.packages('FGNet', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
- FEA_tools - FGNet data
- GOEvidenceCodes - FGNet data
- groupTypes - FGNet data
- organisms - FGNet data
On BioConductor:FGNet-3.47.0(bioc 3.24)FGNet-3.46.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
annotationgopathwaysgenesetenrichmentnetworkvisualizationfunctionalgenomicsnetworkenrichmentclustering
Last updated from:567511106f (on RELEASE_3_23). Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 235 | ||
| linux-devel-x86_64 | WARNING | 254 | ||
| source / vignettes | OK | 264 | ||
| linux-release-x86_64 | WARNING | 256 | ||
| macos-release-arm64 | WARNING | 150 | ||
| macos-oldrel-arm64 | WARNING | 129 | ||
| windows-devel | WARNING | 154 | ||
| windows-release | WARNING | 166 | ||
| windows-oldrel | WARNING | 212 | ||
| wasm-release | OK | 195 |
Exports:analyzeNetworkclustersDistancefea_gagefea_gtLinkerfea_gtLinker_getResultsfea_topGOfea2incidMatFGNet_GUIFGNet_reportformat_davidformat_resultsfunctionalNetworkgetTermskeywordsTermplotGoAncestorsreadGeneTermSets
Dependencies:clicpp11gluehwriterigraphlatticelifecyclemagrittrMatrixpkgconfigplotrixplyrpngR.methodsS3R.ooR.utilsRColorBrewerRcppreshape2rlangstringistringrvctrsXML
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Functional gene networks derived from biological enrichment analyses | FGNet-package FGNet |
| Analyze Functional Network | analyzeNetwork |
| Plots distances between metagroups. | clustersDistance plotMetagroupsDistance |
| FEA - GAGE | fea_gage |
| FEA - Gene-Term Linker | fea_gtLinker fea_gtLinker_getResults getResults_gtLinker query_gtLinker |
| FEA - topGO | fea_topGO |
| Transforms FEA output into incidence matrices. | adjMatrix fea2incidMat toMatrix |
| FGNet graphical user interface | FGNet_GUI |
| FGNet report | FGNet_report report_david report_gtLinker |
| Format DAVID output | format_david getResults_david |
| Format FEA results from external tools. | format_results |
| Creates and plots the functional gene network. | functionalNetwork intersectionNetwork |
| Get terms in the metagroups/clusters. | getTerms |
| Select keyword term | keywordsTerm |
| FGNet data | FEA_tools GOEvidenceCodes groupTypes organisms |
| Plot GO term ancestors | plotGoAncestors |
| Read gene-term sets | readGeneTermSets |