Overview | Demostration: a local data.frame with 5 columns | Demonstration: a remote GWAS file with 34 columns | Session Info
Package: igvR 1.33.2
Arkadiusz Gladki
igvR: igvR: integrative genomics viewer
Access to igv.js, the Integrative Genomics Viewer running in a web browser.
Authors:
igvR_1.33.2.tar.gz
igvR_1.33.2.zip(r-4.7)igvR_1.33.2.zip(r-4.6)igvR_1.33.2.zip(r-4.5)
igvR_1.33.2.tgz(r-4.6-any)igvR_1.33.2.tgz(r-4.5-any)
igvR_1.33.2.tar.gz(r-4.7-any)igvR_1.33.2.tar.gz(r-4.6-any)
igvR_1.33.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
igvR/json (API)
| # Install 'igvR' in R: |
| install.packages('igvR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/gladkia/igvr/issues
Pkgdown/docs site:https://gladkia.github.io
On BioConductor:igvR-1.33.2(bioc 3.24)igvR-1.32.0(bioc 3.23)
visualizationthirdpartyclientgenomebrowsers
Last updated from:3dbd016bae. Checks:1 ERROR, 9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 224 | ||
| linux-devel-x86_64 | OK | 426 | ||
| source / vignettes | OK | 248 | ||
| linux-release-x86_64 | OK | 365 | ||
| macos-release-arm64 | OK | 216 | ||
| macos-oldrel-arm64 | OK | 243 | ||
| windows-devel | OK | 319 | ||
| windows-release | OK | 298 | ||
| windows-oldrel | OK | 307 | ||
| wasm-release | OK | 192 |
Exports:BedpeInteractionsTrackCramTrackcurrently.supported.stock.genomesDataFrameAnnotationTrackDataFrameQuantitativeTrackdisplayTrackenableMotifLogoPopupsGenomicAlignmentTrackgetGenomicRegiongetSupportedGenomesgetTrackNamesGFF3TrackGRangesAnnotationTrackGRangesQuantitativeTrackGWASTrackGWASUrlTrackigvRparseAndValidateGenomeSpecpingQuantitativeTrackRemoteAlignmentTrackremoveTracksByNamesaveToSVGsetCustomGenomesetGenomesetTrackClickFunctionsetTrackHeightshowGenomicRegionshowTrackLabelsTracktrackInfotrackSizeUCSCBedAnnotationTrackUCSCBedGraphQuantitativeTrackurl.existsVariantTrackzoomInzoomOut
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBrowserVizBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttpuvhttrIRangesjsonliteKEGGRESTlambda.rlaterlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslotelpkgconfigpngpromisesR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsysVariantAnnotationvctrsXMLXVectoryaml
GWAS Tracks
Last update: 2026-05-01
Started: 2022-07-28
Introduction: a simple demo
Overview | Load the libraries we need | Display a list of the currently supported genomes | Display MYC | Create and display minimal 1-row data.frame centered below MYC on chr8 | Create and display a simulated quantitative (bedGraph) track | Zoom out by direct manipulation of the currently displayed region | Zoom out and by function calls | Session Info
Last update: 2026-05-01
Started: 2022-07-24
Obtain and Display H3K27ac K562 track from the AnnotationHub
Overview | Display a genomic region of interest in igvR | Query the AnnotationHub | Select Two Resources: boadPeaks and fc bigwig | broadPeaks: subset and display | bigWig: subset and display | Session Info
Last update: 2026-05-01
Started: 2022-07-25
Obtain and Display H3K4Me3 K562 track from UCSC table browser
Overview | Display a genomic region of interest in igvR | Obtain the coordinates | Navigate the Table Browser | Examine the Data | Download the Data | Read the data into R | Create and Display a Quantitative Track | Session Info
Last update: 2026-05-01
Started: 2022-07-24
Paired-end Interaction Tracks
Overview | Example | Code | Display | Session Info
Last update: 2026-05-01
Started: 2022-07-24
Use a Custom Genome
Overview | Explicit loading of "custom" hg38 | Use the SARS-CoV-2 genome | Configure and run an nginx webserver, with CORS and Byte-Range support | CORS: cross-origin resource sharing | Byte-range support | A sample nginx configuration. | Run nginx out of a docker container. | Session Info
Last update: 2026-05-01
Started: 2022-07-24
Use a Stock Genome
Overview | Demonstration | Display | Session Info
Last update: 2026-05-01
Started: 2022-07-24
Visualizing CRAM Alignments
Overview | Load the libraries | Initialize igvR | Scenario 1: Loading a Remote CRAM File | Scenario 2: Visualizing Local CRAM Files | Step 1: Start a Local Web Server | Step 2: Load the Track using "localhost" | Session Info
Last update: 2026-05-01
Started: 2025-12-17
Explore CTCF ChIP-seq alignments, MACS2 narrowPeaks, Motif Matching and H3K4me3 methylation
Overview | Initialize igvR | Load alignments for the currently displayed genomic region | Display the alignment | Narrow Peaks from MACS | Motif Matching | Display the Matches | H3K4Me3 Histone Marks | Zoom in to one interesting, and possibly functional CTCF binding site
Last update: 2025-12-17
Started: 2022-07-24
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Constructor for BedpeInteractionsTrack | .BedpeInteractionsTrack BedpeInteractionsTrack BedpeInteractionsTrack-class |
| Constructor for CramTrack | .CramTrack CramTrack CramTrack-class |
| currently.supported.stock.genomes | currently.supported.stock.genomes |
| Constructor for DataFrameAnnotationTrack | .DataFrameAnnotationTrack DataFrameAnnotationTrack DataFrameAnnotationTrack-class |
| Constructor for DataFrameQuantitativeTrack | .DataFrameQuantitativeTrack DataFrameQuantitativeTrack DataFrameQuantitativeTrack-class |
| display the specified track in igv | displayTrack displayTrack,igvR-method |
| turn mottif log popups on or off | enableMotifLogoPopups enableMotifLogoPopups,igvR-method |
| Constructor for GenomicAlignmentTrack | .GenomicAlignmentTrack GenomicAlignmentTrack GenomicAlignmentTrack-class |
| Obtain the chromosome and coordiates of the currently displayed genomic region. | getGenomicRegion getGenomicRegion,igvR-method |
| Get the shorthand codes (eg, "hg38") for the genomes currently supported by our use of igv.js | getSupportedGenomes getSupportedGenomes,igvR-method |
| Get the names of all the tracks currently displayed in igv | getTrackNames getTrackNames,igvR-method |
| Constructor for GFF3Track | .GFF3Track GFF3Track GFF3Track-class |
| Constructor for GRangesAnnotationTrack | .GRangesAnnotationTrack GRangesAnnotationTrack GRangesAnnotationTrack-class |
| Constructor for GRangesQuantitativeTrack | .GRangesQuantitativeTrack GRangesQuantitativeTrack GRangesQuantitativeTrack-class |
| Constructor for GWASTrack | .GWASTrack .GWASUrlTrack GWASTrack GWASTrack-class |
| Constructor for GWASUrlTrack | GWASUrlTrack |
| Constructor for igvAnnotationTrack | .igvAnnotationTrack igvAnnotationTrack igvAnnotationTrack-class |
| Create an igvR object | .igvR igvR igvR-class |
| parseAndValidateGenomeSpec | parseAndValidateGenomeSpec |
| Test the connection between your R session and the webapp | ping ping,igvR-method |
| Constructor for QuantitativeTrack | .QuantitativeTrack QuantitativeTrack QuantitativeTrack-class |
| Constructor for RemoteAlignmentTrack | .RemoteAlignmentTrack RemoteAlignmentTrack RemoteAlignmentTrack-class |
| Remove named tracks | removeTracksByName removeTracksByName,igvR-method |
| Get entire igv browser image in svg | saveToSVG saveToSVG,igvR-method |
| Specify the reference genome you wish to use, via full specification of all urls | setCustomGenome setCustomGenome,igvR-method |
| Specify the reference genome, currently limited to hg38, hg19, mm10, tair10. | setGenome setGenome,igvR-method |
| Specify (supply) the javascript function run on track click event | setTrackClickFunction setTrackClickFunction,igvR-method |
| Remove named tracks | setTrackHeight setTrackHeight,igvR-method |
| Set the visible region, by explicit chromLoc string, or by named features in any curently loaded annotation tracks | showGenomicRegion showGenomicRegion,igvR-method |
| Hide or show igv track labels | showTrackLabels showTrackLabels,igvR-method |
| Constructor for Track | .Track Track Track-class |
| Get basic info about a track: its type, file format, source and S4 class name | trackInfo trackInfo,Track-method |
| Retrieve the size of the BedpeInteractionsTrack | trackSize,BedpeInteractionsTrack-method |
| Retrieve the size of the DataFrameAnnotationTrack | trackSize,DataFrameAnnotationTrack-method |
| Retrieve the size of the DataFrameQuantitativeTrack | trackSize,DataFrameQuantitativeTrack-method |
| Retrieve the size of the GenomicAlignmentTrack | trackSize,GenomicAlignmentTrack-method |
| Retrieve the size of the GFF3Track | trackSize,GFF3Track-method |
| Retrieve the size of the GRangesAnnotationTrack | trackSize,GRangesAnnotationTrack-method |
| Retrieve the size of the GRangesQuantitativeTrack | trackSize,GRangesQuantitativeTrack-method |
| Retrieve the size of the GWASTrack | trackSize,GWASTrack-method |
| Retrieve the size of the GWASUrlTrack | trackSize,GWASUrlTrack-method |
| Retrieve the size of the QuantitativeTrack | trackSize trackSize,QuantitativeTrack-method |
| Retrieve the size of theUCSCBedAnnotationTrack | trackSize,UCSCBedAnnotationTrack-method |
| Retrieve the size of the UCSCBedGraphQuantitativeTrack | trackSize,UCSCBedGraphQuantitativeTrack-method |
| Retrieve the size of the VariantTrack | trackSize,VariantTrack-method |
| Constructor for UCSCBedAnnotationTrack | .UCSCBedAnnotationTrack UCSCBedAnnotationTrack UCSCBedAnnotationTrack-class |
| Constructor for UCSCBedGraphQuantitativeTrack | .UCSCBedGraphQuantitativeTrack UCSCBedGraphQuantitativeTrack UCSCBedGraphQuantitativeTrack-class |
| url.exists | url.exists |
| Constructor for VariantTrack | VariantTrack VariantTrack-class |
| zoom the genome view in by a factor of 2 | zoomIn zoomIn,igvR-method |
| zoom the genome view out by a factor of 2 | zoomOut zoomOut,igvR-method |
