Package: trackViewer 1.41.3
Jianhong Ou
trackViewer: A R/Bioconductor package with web interface for drawing elegant interactive tracks or lollipop plot to facilitate integrated analysis of multi-omics data
Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.
Authors:
trackViewer_1.41.3.tar.gz
trackViewer_1.41.3.zip(r-4.5)trackViewer_1.41.3.zip(r-4.4)trackViewer_1.41.3.zip(r-4.3)
trackViewer_1.41.3.tgz(r-4.4-any)trackViewer_1.41.3.tgz(r-4.3-any)
trackViewer_1.41.3.tar.gz(r-4.5-noble)trackViewer_1.41.3.tar.gz(r-4.4-noble)
trackViewer_1.41.3.tgz(r-4.4-emscripten)trackViewer_1.41.3.tgz(r-4.3-emscripten)
trackViewer.pdf |trackViewer.html✨
trackViewer/json (API)
NEWS
| # Install 'trackViewer' in R: |
| install.packages('trackViewer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:trackViewer-1.41.0(bioc 3.20)trackViewer-1.40.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 23 days agofrom:220798f786
Exports:addArrowMarkaddGuideLineaddInteractionAnnotationARAbrowseTracksbrowseTracksOutputcoverageGRdandelion.plotgeneModelFromTxdbgeneTrackgetCurTrackViewportgetGeneIDsFromTxDbgetLocationgi2trackgieStainGIoperatorGRoperatorideogramPlotimportBamimportDataimportGInteractionsimportScorelistChromosomeslistResolutionsloadIdeogramlolliplotloopBouquetPlotmdsPlotoptimizeStyleparse2GRangesparseWIGplotGRangesreducerenderbrowseTracksseqlevelsseqlevelsStyleseqlevelsStyle<-setTrackStyleParamsetTrackViewerStyleParamsetTrackXscaleParamsetTrackYaxisParamshowtrackListtrackViewerStyleview3dStructureviewGeneviewTracks
Dependencies:abindAnnotationDbiAnnotationFilteraskpassbackportsbase64encBHBiobaseBiocFileCacheBiocGenericsBiocIOBiocParallelbiomaRtBiostringsbiovizBasebitbit64bitopsblobBSgenomebslibcachemcheckmatecliclustercodetoolscolorspacecpp11crayoncurldata.tableDBIdbplyrDelayedArraydeldirdichromatdigestdplyrensembldbevaluatefansifarverfastmapfilelockfontawesomeforeignformatRFormulafsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2gluegridExtragrImportgtableGvizhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrhttr2igraphInteractionSetinterpIRangesisobandjpegjquerylibjsonliteKEGGRESTknitrlabelinglambda.rlatticelatticeExtralazyevallifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimemunsellnlmennetopensslpillarpkgconfigplogrplotrixpngprettyunitsprogressProtGenericspurrrR6rappdirsRColorBrewerRcppRcppEigenRCurlrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangrmarkdownrpartRsamtoolsRSQLiterstudioapirtracklayerS4ArraysS4VectorssassscalessnowSparseArraystrawrstringistringrSummarizedExperimentsystibbletidyrtidyselecttinytextxdbmakerUCSC.utilsutf8VariantAnnotationvctrsviridisviridisLitewithrxfunXMLxml2XVectoryamlzlibbioc
trackViewer Vignette: change the track styles
Rendered fromchangeTracksStyles.Rmdusingknitr::rmarkdownon Jun 18 2024.Last update: 2024-02-17
Started: 2021-04-01
trackViewer Vignette: dandelionPlot
Rendered fromdandelionPlot.Rmdusingknitr::rmarkdownon Jun 18 2024.Last update: 2021-04-04
Started: 2021-04-01
trackViewer Vignette: lollipopPlot
Rendered fromlollipopPlot.Rmdusingknitr::rmarkdownon Jun 18 2024.Last update: 2024-06-17
Started: 2021-04-01
trackViewer Vignette: overview
Rendered fromtrackViewer.Rmdusingknitr::rmarkdownon Jun 18 2024.Last update: 2024-02-08
Started: 2015-10-02
trackViewer Vignette: plot interaction data
Rendered fromplotInteractionData.Rmdusingknitr::rmarkdownon Jun 18 2024.Last update: 2024-05-21
Started: 2021-04-01
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Minimal designed plotting tool for genomic data | trackViewer-package trackViewer |
| Add arrow mark to the figure at a given position | addArrowMark |
| Add guide lines to the tracks | addGuideLine |
| Add annotation markers to the figure at a given position | addInteractionAnnotation |
| Aggregate Region Analysis | ARA |
| browse tracks | browseTracks |
| Shiny bindings for browseTracks | browseTracks-shiny browseTracksOutput renderbrowseTracks |
| calculate coverage | coverageGR |
| dandelion.plots | dandelion.plot |
| Prepare gene model from an object of TxDb | geneModelFromTxdb |
| track from TxDb | geneTrack |
| Get current track viewport | getCurTrackViewport |
| get gene ids by genomic location | getGeneIDsFromTxDb |
| get genomic location by gene symbol | getLocation |
| convert GInteractions to track object | gi2track |
| color sheme for the schema for Chromosome Band (Ideogram) | gieStain |
| GInteractions operator | GIoperator |
| plot GRanges metadata | gridPlot |
| GRanges operator | GRoperator |
| plot ideogram with data | ideogramPlot |
| Reading data from a BAM file | importBam |
| Reading data from a BED or WIG file to RleList | importData |
| Reading data from a ginteractions, hic, cool, or validPairs file | importGInteractions |
| Reading data from a BED or WIG file | importScore |
| plot tracks for single cell RNAseq | importScSeqScore |
| List the available chromosome | listChromosomes |
| List the available resolutions | listResolutions |
| load ideogram from UCSC | loadIdeogram |
| Lolliplots | lolliplot |
| plot GInteractions | loopBouquetPlot |
| Plot genomic interactions by multi-dimensional scaling plot | mdsPlot |
| Optimize the style of plot | optimizeStyle |
| parse text into GRanges | parse2GRanges |
| convert WIG format track to BED format track | parseWIG |
| plot GRanges data | plotGRanges |
| plot ideogram | plotIdeo |
| plot ideogram with data for one chromosome | plotOneIdeo |
| Class '"pos"' | pos pos-class |
| Reduce method for 'GInteractions' | reduce,GInteractions reduce,GInteractions-method |
| List of tracks | seqlevelsStyle<-,trackList-method trackList trackList-class |
| Class '"trackStyle"' | $,track-method $<-,track-method seqlevels,track-method seqlevelsStyle,track-method seqlevelsStyle<-,track-method setTrackStyleParam setTrackStyleParam,track,character,ANY-method setTrackStyleParam,track,character-method setTrackXscaleParam setTrackXscaleParam,track,character,ANY-method setTrackXscaleParam,track,character-method setTrackYaxisParam setTrackYaxisParam,track,character,ANY-method setTrackYaxisParam,track,character-method show,track-method track track-class trackStyle trackStyle-class |
| Class '"trackViewerStyle"' | setTrackViewerStyleParam setTrackViewerStyleParam,trackViewerStyle,character,ANY-method setTrackViewerStyleParam,trackViewerStyle,character-method trackViewerStyle trackViewerStyle-class |
| Plot xyz data in 2d or 3d | view3dStructure |
| plot tracks based on gene name | viewGene |
| plot the tracks | viewTracks |
| Class '"xscale"' | xscale xscale-class |
| Class '"yaxisStyle"' | yaxisStyle yaxisStyle-class |
