Package: scanMiRApp 1.19.0
Pierre-Luc Germain
scanMiRApp: scanMiR shiny application
A shiny interface to the scanMiR package. The application enables the scanning of transcripts and custom sequences for miRNA binding sites, the visualization of KdModels and binding results, as well as browsing predicted repression data. In addition contains the IndexedFst class for fast indexed reading of large GenomicRanges or data.frames, and some utilities for facilitating scans and identifying enriched miRNA-target pairs.
Authors:
scanMiRApp_1.19.0.tar.gz
scanMiRApp_1.19.0.zip(r-4.7)scanMiRApp_1.19.0.zip(r-4.6)scanMiRApp_1.19.0.zip(r-4.5)
scanMiRApp_1.19.0.tgz(r-4.6-any)scanMiRApp_1.19.0.tgz(r-4.5-any)
scanMiRApp_1.19.0.tar.gz(r-4.7-any)scanMiRApp_1.19.0.tar.gz(r-4.6-any)
scanMiRApp_1.19.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
scanMiRApp/json (API)
| # Install 'scanMiRApp' in R: |
| install.packages('scanMiRApp', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:scanMiRApp-1.19.0(bioc 3.24)scanMiRApp-1.18.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
mirnasequencematchingguishinyapps
Last updated from:7b6d92e167. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 448 | ||
| linux-devel-x86_64 | NOTE | 641 | ||
| source / vignettes | OK | 503 | ||
| linux-release-x86_64 | NOTE | 676 | ||
| macos-release-arm64 | NOTE | 443 | ||
| macos-oldrel-arm64 | NOTE | 418 | ||
| windows-devel | NOTE | 552 | ||
| windows-release | NOTE | 467 | ||
| windows-oldrel | NOTE | 570 | ||
| wasm-release | OK | 398 |
Exports:as.data.framecolnamesenrichedMirTxPairsgetTranscriptSequenceheadloadIndexedFstncolnrowplotSitesOnUTRrunFullScansaveIndexedFstScanMiRAnnoscanMiRAppscanMiRserverscanMiRuishowsummary
Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobbslibcachemcigarilloclicodetoolscommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrDTensembldbevaluatefarverfastmapfilelockfontawesomeformatRfsfstfstcorefutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigplotlypngprettyunitsprogresspromisesProtGenericspurrrpwalignR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrintrojsrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesscanMiRscanMiRDataSeqinfoseqLogoshinyshinycssloadersshinydashboardshinyjquisnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8vctrsviridisLitewaiterwithrxfunXMLxml2xtableXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| enrichedMirTxPairs | enrichedMirTxPairs |
| Example 'fake' TxDb object | fakeTxDb |
| getTranscriptSequence | getTranscriptSequence |
| IndexedFst | $,IndexedFst-method as.data.frame,IndexedFst-method colnames,IndexedFst-method head,IndexedFst-method IndexedFst IndexedFst-class length,IndexedFst-method lengths,IndexedFst-method names,IndexedFst-method ncol,IndexedFst-method nrow,IndexedFst-method show,IndexedFst-method summary,IndexedFst-method [,IndexedFst,ANY,ANY,ANY-method [[,IndexedFst,ANY,ANY-method |
| Saving and loading IndexedFst | loadIndexedFst saveIndexedFst |
| plotSitesOnUTR | plotSitesOnUTR |
| runFullScan | runFullScan |
| ScanMiRAnno | ScanMiRAnno ScanMiRAnno-class |
| Methods for the 'ScanMiRAnno' class | ScanMiRAnno-methods show,ScanMiRAnno-method summary,ScanMiRAnno-method |
| scanMiRApp A wrapper for launching the scanMiRApp shiny app | scanMiRApp |
| scanMiRserver | scanMiRserver |
| scanMiRui | scanMiRui |
