Package: igvR 1.27.0
Arkadiusz Gladki
igvR: igvR: integrative genomics viewer
Access to igv.js, the Integrative Genomics Viewer running in a web browser.
Authors:
igvR_1.27.0.tar.gz
igvR_1.27.0.zip(r-4.5)igvR_1.27.0.zip(r-4.4)igvR_1.27.0.zip(r-4.3)
igvR_1.27.0.tgz(r-4.4-any)igvR_1.27.0.tgz(r-4.3-any)
igvR_1.27.0.tar.gz(r-4.5-noble)igvR_1.27.0.tar.gz(r-4.4-noble)
igvR_1.27.0.tgz(r-4.4-emscripten)igvR_1.27.0.tgz(r-4.3-emscripten)
igvR.pdf |igvR.html✨
igvR/json (API)
NEWS
| # 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:https://gladkia.github.io
On BioConductor:igvR-1.27.0(bioc 3.21)igvR-1.26.0(bioc 3.20)
visualizationthirdpartyclientgenomebrowsers
Last updated 2 months agofrom:e490c15f79. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 21 2024 |
| R-4.5-win | NOTE | Nov 21 2024 |
| R-4.5-linux | NOTE | Dec 21 2024 |
| R-4.4-win | NOTE | Nov 21 2024 |
| R-4.4-mac | NOTE | Dec 21 2024 |
| R-4.3-win | NOTE | Nov 21 2024 |
| R-4.3-mac | NOTE | Dec 21 2024 |
Exports:BedpeInteractionsTrackcurrently.supported.stock.genomesDataFrameAnnotationTrackDataFrameQuantitativeTrackdisplayTrackenableMotifLogoPopupsGenomicAlignmentTrackgetGenomicRegiongetSupportedGenomesgetTrackNamesGFF3TrackGRangesAnnotationTrackGRangesQuantitativeTrackGWASTrackGWASUrlTrackigvRparseAndValidateGenomeSpecpingQuantitativeTrackRemoteAlignmentTrackremoveTracksByNamesaveToSVGsetCustomGenomesetGenomesetTrackClickFunctionsetTrackHeightshowGenomicRegionshowTrackLabelsTracktrackInfotrackSizeUCSCBedAnnotationTrackUCSCBedGraphQuantitativeTrackurl.existsVariantTrackzoomInzoomOut
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBrowserVizBSgenomecachemclicodetoolscpp11crayoncurlDBIDelayedArrayfastmapformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttpuvhttrIRangesjsonliteKEGGRESTlambda.rlaterlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpkgconfigplogrpngpromisesR6RColorBrewerRcppRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorssnowSparseArraySummarizedExperimentsysUCSC.utilsVariantAnnotationvctrsXMLXVectoryamlzlibbioc
Explore CTCF ChIP-seq alignments, MACS2 narrowPeaks, Motif Matching and H3K4me3 methylation
Rendered fromv03.ctcfChIP.Rmdusingknitr::rmarkdownon Dec 21 2024.Last update: 2022-07-24
Started: 2022-07-24
GWAS Tracks
Rendered fromv07.gwas.Rmdusingknitr::rmarkdownon Dec 21 2024.Last update: 2022-07-28
Started: 2022-07-28
Introduction: a simple demo
Rendered fromv00.basicIntro.Rmdusingknitr::rmarkdownon Dec 21 2024.Last update: 2022-07-24
Started: 2022-07-24
Obtain and Display H3K27ac K562 track from the AnnotationHub
Rendered fromv06.annotationHub.Rmdusingknitr::rmarkdownon Dec 21 2024.Last update: 2022-09-06
Started: 2022-07-25
Obtain and Display H3K4Me3 K562 track from UCSC table browser
Rendered fromv05.ucscTableBrowser.Rmdusingknitr::rmarkdownon Dec 21 2024.Last update: 2023-10-09
Started: 2022-07-24
Paired-end Interaction Tracks
Rendered fromv04.pairedEnd.Rmdusingknitr::rmarkdownon Dec 21 2024.Last update: 2022-07-24
Started: 2022-07-24
Use a Custom Genome
Rendered fromv02.customGenome.Rmdusingknitr::rmarkdownon Dec 21 2024.Last update: 2022-07-24
Started: 2022-07-24
Use a Stock Genome
Rendered fromv01.stockGenome.Rmdusingknitr::rmarkdownon Dec 21 2024.Last update: 2022-07-24
Started: 2022-07-24
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Constructor for BedpeInteractionsTrack | .BedpeInteractionsTrack BedpeInteractionsTrack BedpeInteractionsTrack-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 |
