Package: func2vis 1.0-3
func2vis: Clean and Visualize Over Expression Results from 'ConsensusPathDB'
Provides functions to have visualization and clean-up of enriched gene ontologies (GO) terms, protein complexes and pathways (obtained from multiple databases) using 'ConsensusPathDB' from gene set over-expression analysis. Performs clustering of pathway based on similarity of over-expressed gene sets and visualizations similar to Ingenuity Pathway Analysis (IPA) when up and down regulated genes are known. The methods are described in a paper currently submitted by Orecchioni et al, 2020 in Nanoscale.
Authors:
func2vis_1.0-3.tar.gz
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func2vis_1.0-3.tgz(r-4.4-any)func2vis_1.0-3.tgz(r-4.3-any)
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func2vis.pdf |func2vis.html✨
func2vis/json (API)
| # Install 'func2vis' in R: |
| install.packages('func2vis', repos = c('https://raghvendra5688.r-universe.dev', 'https://cloud.r-project.org')) |
- enriched_goterms - Sample Enriched Gene Ontologies (GO) Terms
- enriched_pathways - Sample Enriched Pathways
- enriched_pc - Sample Enriched Protein Complexes
- t.tests.treatment.sign - List of differentially expressed genes
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 years agofrom:59f41fa989. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 28 2024 |
| R-4.5-win | OK | Aug 28 2024 |
| R-4.5-linux | OK | Aug 28 2024 |
| R-4.4-win | OK | Aug 28 2024 |
| R-4.4-mac | OK | Aug 28 2024 |
| R-4.3-win | OK | Aug 28 2024 |
| R-4.3-mac | OK | Aug 28 2024 |
Exports:clean_go_termsclean_pathwaysclean_pcplot_go_termsplot_pathwaysplot_pathways_stacked_barplot
Dependencies:askpassbase64encbrewbriobslibcachemcallrclicliprclustercolorspacecommonmarkcpp11crayoncredentialscurldescdevtoolsdiffobjdigestdownlitellipsisevaluatefansifarverfastmapfontawesomefsgertggplot2ggrepelghgitcredsgluegtablehighrhtmltoolshtmlwidgetshttpuvhttr2igraphiniisobandjquerylibjsonliteknitrlabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimeminiUImunsellnlmeopensslpillarpkgbuildpkgconfigpkgdownpkgloadpraiseprettyunitsprocessxprofvispromisespspurrrR6raggrandomcoloRrappdirsrcmdcheckRColorBrewerRcpprematch2remotesrlangrmarkdownroxygen2rprojrootrstudioapiRtsnerversionssassscalessessioninfoshinysourcetoolsstringistringrsyssystemfontstestthattextshapingtibbletinytexurlcheckerusethisutf8V8vctrsviridisLitewaldowhiskerwithrxfunxml2xopenxtableyamlzip
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Clean Gene Ontologies (GO) Terms | clean_go_terms |
| Clean Enriched Pathways | clean_pathways |
| Clean Enriched Protein Complexes | clean_pc |
| Sample Enriched Gene Ontologies (GO) Terms | enriched_goterms |
| Sample Enriched Pathways | enriched_pathways |
| Sample Enriched Protein Complexes | enriched_pc |
| Bupple Plot for GO Terms | plot_go_terms |
| Plot clean enriched pathways as a bubble plot | plot_pathways |
| Stacked Barplot of Cleaned Pathways | plot_pathways_stacked_barplot |
| List of differentially expressed genes | t.tests.treatment.sign |
