Package: FGNet 3.41.0
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_3.41.0.tar.gz
FGNet_3.41.0.zip(r-4.5)FGNet_3.41.0.zip(r-4.4)FGNet_3.41.0.zip(r-4.3)
FGNet_3.41.0.tgz(r-4.4-any)FGNet_3.41.0.tgz(r-4.3-any)
FGNet_3.41.0.tar.gz(r-4.5-noble)FGNet_3.41.0.tar.gz(r-4.4-noble)
FGNet_3.41.0.tgz(r-4.4-emscripten)FGNet_3.41.0.tgz(r-4.3-emscripten)
FGNet.pdf |FGNet.html✨
FGNet/json (API)
NEWS
| # Install 'FGNet' in R: |
| install.packages('FGNet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- FEA_tools - FGNet data
- GOEvidenceCodes - FGNet data
- groupTypes - FGNet data
- organisms - FGNet data
On BioConductor:FGNet-3.41.0(bioc 3.21)FGNet-3.40.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
annotationgopathwaysgenesetenrichmentnetworkvisualizationfunctionalgenomicsnetworkenrichmentclustering
Last updated 23 days agofrom:a782bd5fd5. Checks:OK: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win | WARNING | Oct 31 2024 |
| R-4.5-linux | WARNING | Oct 31 2024 |
| R-4.4-win | WARNING | Oct 31 2024 |
| R-4.4-mac | WARNING | Oct 31 2024 |
| R-4.3-win | WARNING | Oct 31 2024 |
| R-4.3-mac | WARNING | Oct 31 2024 |
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 |