1. Introduction to FGNet | Biological functional analysis | Functional network | 2. Installation | 3. Creating a network | In R code... | Functional Enrichment Analysis (FEA) | TopGO | GAGE | Other tools | Web analysis | HTML report | Individual networks | 4. Editing and creating new networks | Incidence matrices | Bipartite and intersection network | Terms networks | Genes - Terms networks | 5. Filtering and selecting clusters | Filtering based on a cluster property | Selecting clusters with specific keywords | Selecting specific clusters | Filtering based on a gene-term set property | 6. Other auxiliary functions | analyzeNetwork() | plotGoAncestors() | 7. Acknowledgments | 8. References | Deprecated functionalities: | Graphical User Interface (GUI)
Package: FGNet 3.47.0
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_3.47.0.tar.gz
FGNet_3.47.0.zip(r-4.7)FGNet_3.47.0.zip(r-4.6)FGNet_3.47.0.zip(r-4.5)
FGNet_3.47.0.tgz(r-4.6-any)FGNet_3.47.0.tgz(r-4.5-any)
FGNet_3.47.0.tar.gz(r-4.7-any)FGNet_3.47.0.tar.gz(r-4.6-any)
FGNet_3.47.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FGNet/json (API)
| # Install 'FGNet' in R: |
| install.packages('FGNet', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- 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:b133ae0a21. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 240 | ||
| linux-devel-x86_64 | WARNING | 249 | ||
| source / vignettes | OK | 271 | ||
| linux-release-x86_64 | WARNING | 225 | ||
| macos-release-arm64 | WARNING | 116 | ||
| macos-oldrel-arm64 | WARNING | 126 | ||
| windows-devel | WARNING | 160 | ||
| windows-release | WARNING | 161 | ||
| windows-oldrel | WARNING | 160 | ||
| wasm-release | OK | 229 |
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 |