Package: mirIntegrator 1.37.0
Diana Diaz
mirIntegrator: Integrating microRNA expression into signaling pathways for pathway analysis
Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.
Authors:
mirIntegrator_1.37.0.tar.gz
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mirIntegrator.pdf |mirIntegrator.html✨
mirIntegrator/json (API)
NEWS
| # Install 'mirIntegrator' in R: |
| install.packages('mirIntegrator', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/datad/mirintegrator/issues
- GSE43592_mRNA - Top table of preprocessed mRNA of GSE43592 dataset.
- GSE43592_miRNA - Top table of preprocessed miRNA of GSE43592 dataset.
- augmented_pathways - Signaling pathways augmented with miRNA.
- kegg_pathways - List of KEGG signaling pathways of human.
- mirTarBase - MicroRNA-target interactions in human.
- names_pathways - List of KEGG signaling pathways' names.
On BioConductor:mirIntegrator-1.37.0(bioc 3.21)mirIntegrator-1.36.0(bioc 3.20)
networkmicroarraygraphandnetworkpathwayskegg
Last updated 4 months agofrom:f0be6940d3. Checks:1 OK, 7 NOTE. Indexed: yes.
| Target | Result | Latest binary |
|---|---|---|
| Doc / Vignettes | OK | Feb 27 2025 |
| R-4.5-win | NOTE | Feb 27 2025 |
| R-4.5-mac | NOTE | Feb 27 2025 |
| R-4.5-linux | NOTE | Feb 27 2025 |
| R-4.4-win | NOTE | Feb 27 2025 |
| R-4.4-mac | NOTE | Feb 27 2025 |
| R-4.3-win | NOTE | Feb 27 2025 |
| R-4.3-mac | NOTE | Feb 27 2025 |
Exports:integrate_mirpathways2pdfplot_augmented_pathwayplot_changesmallest_pathway
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobbootcachemclicolorspacecpp11crayoncurlDBIfansifarverfastmapgenericsGenomeInfoDbGenomeInfoDbDataggplot2gluegraphgtablehttrIRangesisobandjsonliteKEGGgraphKEGGRESTlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslorg.Hs.eg.dbpillarpkgconfigplogrpngR6RColorBrewerRCurlRgraphvizrlangROntoToolsRSQLiteS4VectorsscalessystibbleUCSC.utilsutf8vctrsviridisLitewithrXMLXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Signaling pathways augmented with miRNA. | augmented_pathways |
| Top table of preprocessed miRNA of GSE43592 dataset. | GSE43592_miRNA |
| Top table of preprocessed mRNA of GSE43592 dataset. | GSE43592_mRNA |
| Produce augmented pathways | integrate_mir |
| List of KEGG signaling pathways of human. | kegg_pathways |
| MicroRNA-target interactions in human. | mirTarBase |
| List of KEGG signaling pathways' names. | names_pathways |
| Export augmented pathways to pdf | pathways2pdf |
| Plotting of augmented pathway | plot_augmented_pathway |
| Plotting the change in pathways order | plot_change |
| Get the smallest pathway | smallest_pathway |
