Package: scanMiRApp 1.18.0

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:Pierre-Luc Germain [cre, aut], Michael Soutschek [aut], Fridolin Gross [ctb]

scanMiRApp_1.18.0.tar.gz
scanMiRApp_1.18.0.zip(r-4.7-any)scanMiRApp_1.18.0.zip(r-4.6-any)scanMiRApp_1.18.0.zip(r-4.5-any)
scanMiRApp_1.18.0.tgz(r-4.6-any)scanMiRApp_1.18.0.tgz(r-4.5-any)
scanMiRApp_1.18.0.tar.gz(r-4.7-any)scanMiRApp_1.18.0.tar.gz(r-4.6-any)
scanMiRApp_1.18.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
scanMiRApp/json (API)

# Install 'scanMiRApp' in R:
install.packages('scanMiRApp', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:scanMiRApp-1.19.2(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

4.70 score 25 scripts 460 downloads 17 exports 147 dependencies

Last updated from:e406342b32 (on RELEASE_3_23). Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksWARNING353
linux-develNOTE649
source / vignettesOK378
linux-releaseNOTE676
macos-releaseNOTE427
macos-oldrelNOTE410
windows-develNOTE521
windows-releaseNOTE483
windows-oldrelNOTE466
wasm-releaseOK348

Exports:as.data.framecolnamesenrichedMirTxPairsgetTranscriptSequenceheadloadIndexedFstncolnrowplotSitesOnUTRrunFullScansaveIndexedFstScanMiRAnnoscanMiRAppscanMiRserverscanMiRuishowsummary

Dependencies:abindAnnotationDbiAnnotationFilterAnnotationHubaskpassbase64encBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIOBiocManagerBiocParallelBiocVersionbiomaRtBiostringsbitbit64bitopsblobbslibcachemcigarilloclicodetoolscommonmarkcowplotcpp11crayoncrosstalkcurldata.tableDBIdbplyrDelayedArraydigestdplyrDTensembldbevaluatefarverfastmapfilelockfontawesomeformatRfsfstfstcorefutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegtablehighrhmshtmltoolshtmlwidgetshttpuvhttrhttr2IRangesisobandjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlaterlatticelazyevallifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpillarpkgconfigplotlypngprettyunitsprogresspromisesProtGenericspurrrpwalignR6rappdirsRColorBrewerRcppRCurlrestfulrRhtslibrintrojsrjsonrlangrmarkdownRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7sassscalesscanMiRscanMiRDataSeqinfoseqLogoshinyshinycssloadersshinydashboardshinyjquisnowsourcetoolsSparseArraystringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8vctrsviridisLitewaiterwithrxfunXMLxml2xtableXVectoryaml

scanMiRApp: shiny app and related convenience functions
ScanMiRAnno objects | Convenience functions | Obtaining the UTR sequence of a transcript | Plotting sites on the UTR sequence of a transcript | Running a full-transcriptome scan | Detecting enriched miRNA-target pairs | Shiny app | Setting up the application | Multi-threading | Caching | Session info
Rendered fromscanMiRApp.Rmdusingknitr::rmarkdown

Last update: 2021-06-21
Started: 2021-04-16

The IndexedFst class
IndexedFst | Storing GRanges as IndexedFst | More... | Multithreading | Under the hood | Session info
Rendered fromIndexedFST.Rmdusingknitr::rmarkdown

Last update: 2021-06-17
Started: 2021-04-26

Readme and manuals

Help Manual

Help pageTopics
enrichedMirTxPairsenrichedMirTxPairs
Example 'fake' TxDb objectfakeTxDb
getTranscriptSequencegetTranscriptSequence
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 IndexedFstloadIndexedFst saveIndexedFst
plotSitesOnUTRplotSitesOnUTR
runFullScanrunFullScan
ScanMiRAnnoScanMiRAnno ScanMiRAnno-class
Methods for the 'ScanMiRAnno' classScanMiRAnno-methods show,ScanMiRAnno-method summary,ScanMiRAnno-method
scanMiRApp A wrapper for launching the scanMiRApp shiny appscanMiRApp
scanMiRserverscanMiRserver
scanMiRuiscanMiRui