Package: mirIntegrator 1.42.0
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_1.42.0.tar.gz
mirIntegrator_1.42.0.zip(r-4.7)mirIntegrator_1.42.0.zip(r-4.6)mirIntegrator_1.42.0.zip(r-4.5)
mirIntegrator_1.42.0.tgz(r-4.6-any)mirIntegrator_1.42.0.tgz(r-4.5-any)
mirIntegrator_1.42.0.tar.gz(r-4.7-any)mirIntegrator_1.42.0.tar.gz(r-4.6-any)
mirIntegrator_1.42.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
mirIntegrator/json (API)
NEWS
| # Install 'mirIntegrator' in R: |
| install.packages('mirIntegrator', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/datad/mirintegrator/issues
- augmented_pathways - Signaling pathways augmented with miRNA.
- GSE43592_miRNA - Top table of preprocessed miRNA of GSE43592 dataset.
- GSE43592_mRNA - Top table of preprocessed mRNA of GSE43592 dataset.
- 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-1.43.0(bioc 3.24)mirIntegrator-1.42.0(bioc 3.23)
networkmicroarraygraphandnetworkpathwayskegg
Last updated from:6e1c698c28 (on RELEASE_3_23). Checks:1 FAILURE, 7 NOTE, 2 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | FAILURE | 177 | ||
| linux-devel-x86_64 | NOTE | 280 | ||
| source / vignettes | OK | 238 | ||
| linux-release-x86_64 | NOTE | 398 | ||
| macos-release-arm64 | NOTE | 195 | ||
| macos-oldrel-arm64 | NOTE | 159 | ||
| windows-devel | NOTE | 207 | ||
| windows-release | NOTE | 239 | ||
| windows-oldrel | NOTE | 204 | ||
| wasm-release | OK | 151 |
Exports:integrate_mirpathways2pdfplot_augmented_pathwayplot_changesmallest_pathway
Dependencies:AnnotationDbiaskpassBiobaseBiocGenericsBiostringsbitbit64bitopsblobbootcachemclicpp11crayoncurlDBIfarverfastmapgenericsggplot2gluegraphgtablehttrIRangesisobandjsonliteKEGGgraphKEGGRESTlabelinglifecyclememoisemimeopensslorg.Hs.eg.dbpkgconfigpngR6RColorBrewerRCurlRgraphvizrlangROntoToolsRSQLiteS4VectorsS7scalesSeqinfosysvctrsviridisLitewithrXMLXVector
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 |
