Files in paul-shannon/IGV
igvR: integrative genomics viewer

.Rbuildignore

.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS

R/BedpeInteractionsTrack.R R/DataFrameAnnotationTrack.R R/DataFrameQuantitativeTrack.R R/GFF3Track.R R/GRangesAnnotationTrack.R R/GRangesQuantitativeTrack.R R/GWASTrack.R R/GWASUrlTrack.R R/GenomicAlignmentTrack.R R/QuantitativeTrack.R R/RemoteAlignmentTrack.R R/Track.R R/UCSCBedAnnotationTrack.R R/UCSCBedGraphQuantitativeTrack.R R/VariantTrack.R R/genomeSpec.R R/igvAnnotationTrack.R R/igvR.R README.md

_pkgdown.yml

docs/404.html

docs/LICENSE-text.html

docs/articles/alzheimersVariantsNearMEF2C.html

docs/articles/alzheimersVariantsNearMEF2C_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/basicIntro.html

docs/articles/basicIntro_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/chooseStockOrCustomGenome.html

docs/articles/chooseStockOrCustomGenome_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/ctcf-chip-seq-gata2-252kb-igvR.png

docs/articles/ctcf-chip-seq-igvR.png

docs/articles/ctcfChIP.html

docs/articles/ctcfChIP_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/ctcfChipSeq-old.html

docs/articles/ctcfChipSeq-old_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/ctcfChipSeq.html

docs/articles/ctcfChipSeq_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/customGenome.html

docs/articles/customGenome_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/igv-vignette.png

docs/articles/igvR-basicDemo.png

docs/articles/igvR-ctcf-vignette-zoomedIn.png

docs/articles/igvR-ctcf-vignette-zoomedOut.png

docs/articles/igvR-ctcf-vignette.png

docs/articles/igvR-mef2c-Alzheimers-demo-zoomedIn.png

docs/articles/igvR-mef2c-Alzheimers-demo.png

docs/articles/igvR.html

docs/articles/images/annotationHub-01.png

docs/articles/images/annotationHub-02.png

docs/articles/images/ctcfBam-01.png

docs/articles/images/ctcfBam-02.png

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docs/articles/images/ctcfBam-07.png

docs/articles/images/ctcfMotif.png

docs/articles/images/gata2-63kb-h3k4me3.png

docs/articles/images/gata2-63kb.png

docs/articles/images/gwas-01.png

docs/articles/images/gwas-02.png

docs/articles/images/gwas-03.png

docs/articles/images/gwas-04.png

docs/articles/images/ucscTableBrowser-getOutput.png

docs/articles/images/ucscTableBrowser.png

docs/articles/images/ucscTableBrowserOutput.png

docs/articles/index.html

docs/articles/pairedEnd.html

docs/articles/pairedEnd.png

docs/articles/pairedEnd_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/stockGenome.html

docs/articles/stockGenome_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/stockGenomes.png

docs/articles/ucscTableBrowser.html

docs/articles/ucscTableBrowser_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/v00.basicIntro.html

docs/articles/v00.basicIntro_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/v01.stockGenome.html

docs/articles/v01.stockGenome_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/v02.customGenome.html

docs/articles/v02.customGenome_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/v03.ctcfChIP.html

docs/articles/v03.ctcfChIP_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/v04.pairedEnd.html

docs/articles/v04.pairedEnd_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/v05.ucscTableBrowser.html

docs/articles/v05.ucscTableBrowser_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/v06.annotationHub.html

docs/articles/v06.annotationHub_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/v07.gwas.html

docs/articles/v07.gwas_files/accessible-code-block-0.0.1/empty-anchor.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/ctcf-chip-seq-igvR.png

docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js

docs/deps/bootstrap-5.1.0/bootstrap.bundle.min.js.map

docs/deps/bootstrap-5.1.0/bootstrap.min.css

docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js

docs/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map

docs/deps/bootstrap-5.1.3/bootstrap.min.css

docs/deps/data-deps.txt

docs/deps/jquery-3.6.0/jquery-3.6.0.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.map

docs/docsearch.css

docs/docsearch.js

docs/igvR-ctcf-vignette-zoomedIn.png

docs/igvR-ctcf-vignette-zoomedOut.png

docs/igvR-ctcf-vignette.png

docs/index.html

docs/junk

docs/lcApp-APOC1-for-README.png

docs/link.svg

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/BedpeInteractionsTrack-class.html

docs/reference/DataFrameAnnotationTrack-class.html

docs/reference/DataFrameQuantitativeTrack-class.html

docs/reference/GFF3Track-class.html

docs/reference/GRangesAnnotationTrack-class.html

docs/reference/GRangesQuantitativeTrack-class.html

docs/reference/GWASTrack-class.html

docs/reference/GWASUrlTrack-class.html

docs/reference/GenomicAlignmentTrack-class.html

docs/reference/QuantitativeTrack-class.html

docs/reference/RemoteAlignmentTrack-class.html

docs/reference/Rplot001.png

docs/reference/Track-class.html

docs/reference/UCSCBedAnnotationTrack-class.html

docs/reference/UCSCBedGraphQuantitativeTrack-class.html

docs/reference/VariantTrack-class.html

docs/reference/currently.supported.stock.genomes.html

docs/reference/displayTrack.html

docs/reference/enableMotifLogoPopups.html

docs/reference/getGenomicRegion.html

docs/reference/getSupportedGenomes.html

docs/reference/getTrackNames.html

docs/reference/igvAnnotationTrack-class.html

docs/reference/igvR-class.html

docs/reference/index.html

docs/reference/parseAndValidateGenomeSpec.html

docs/reference/ping.html

docs/reference/removeTracksByName.html

docs/reference/saveToSVG.html

docs/reference/setCustomGenome.html

docs/reference/setGenome.html

docs/reference/setTrackClickFunction.html

docs/reference/setTrackHeight.html

docs/reference/showGenomicRegion.html

docs/reference/showTrackLabels.html

docs/reference/trackInfo.html

docs/reference/trackSize-BedpeInteractionsTrack-method.html

docs/reference/trackSize-DataFrameAnnotationTrack-method.html

docs/reference/trackSize-DataFrameQuantitativeTrack-method.html

docs/reference/trackSize-GFF3Track-method.html

docs/reference/trackSize-GRangesAnnotationTrack-method.html

docs/reference/trackSize-GRangesQuantitativeTrack-method.html

docs/reference/trackSize-GWASTrack-method.html

docs/reference/trackSize-GWASUrlTrack-method.html

docs/reference/trackSize-GenomicAlignmentTrack-method.html

docs/reference/trackSize-UCSCBedAnnotationTrack-method.html

docs/reference/trackSize-UCSCBedGraphQuantitativeTrack-method.html

docs/reference/trackSize-VariantTrack-method.html

docs/reference/trackSize.html

docs/reference/url.exists.html

docs/reference/zoomIn.html

docs/reference/zoomOut.html

docs/search.json

docs/sitemap.xml

explore/alignmentTracks/genomicAlignnments.R

explore/alignmentTracks/igvBam.html

explore/alignmentTracks/x.bam

explore/alignmentTracks/x.bam.bai

explore/alignmentTracks/x.sam

explore/alignmentTracks/x2.bam

explore/bedgraph/bedgraph.html

explore/bedgraph/igv-2.13.11.js

explore/bedpeTrack/demo.html

explore/corsExperimentsAndDebugging/bam.html

explore/corsExperimentsAndDebugging/bed-tbi.html

explore/corsExperimentsAndDebugging/bigWig.html

explore/corsExperimentsAndDebugging/igv-data-tbiOnly.html

explore/corsExperimentsAndDebugging/minimalTest.html

explore/corsExperimentsAndDebugging/simpleBed.html

explore/corsExperimentsAndDebugging/simpleVcf.html

explore/corsExperimentsAndDebugging/vcfExampleFromJim.html

explore/customReferenceGenome/christianRohdeDemo.html

explore/customReferenceGenome/makefile

explore/customReferenceGenome/robinsonDemo.html

explore/gff3Track/gff3Demo.html

explore/gff3Track/makefile

explore/gff3Track/smallCustomGFF3.html

explore/gwasTrack/bellenguez-gwas.html

explore/gwasTrack/bellenguez.bed

explore/gwasTrack/carolin.gwas

explore/gwasTrack/gwas-bed.html

explore/gwasTrack/gwas-carolin.html

explore/gwasTrack/gwas-gwas.html

explore/gwasTrack/gwas-jimRobinson-gz.html

explore/gwasTrack/gwas-twoTracks.html

explore/gwasTrack/gwas-yeast-V-colorDisagreement.html

explore/gwasTrack/gwas_sample_tiny.gwas

explore/gwasTrack/igv-2.12.6-patched.js

explore/gwasTrack/igv-2.12.6.js

explore/gwasTrack/igv-2.13.1.js

explore/gwasTrack/igv.min-2.12.6.js

explore/gwasTrack/issue19.R explore/gwasTrackColors/bug.R

explore/gwasTrackColors/data_test/noPPI_reference_MTX_noDrug_avg_logratio_Fitness_minus_ref.csv

explore/gwasTrackColors/data_test/noPPI_reference_noMTX_noDrug_avg_logratio_Fitness_minus_ref.csv

explore/gwasTrackColors/gwas-yeast-V-colorDisagreement.html.gz

explore/gwasTrackColors/igv-2.13.11.js

explore/gwasTrackColors/junk

explore/gwasTrackColors/newColorSupport.html

explore/gwasTrackColors/tbl.gwas.yeast.chrV.tsv

explore/vcfTrack/vcfTrack.html

inst/browserCode/dist/igvApp.html

inst/browserCode/lib/browserviz.js

inst/browserCode/lib/igv-2.12.6-patched.js

inst/browserCode/lib/igv-2.12.6.js

inst/browserCode/lib/igv-2.13.11.js

inst/browserCode/lib/igv-2.13.9.js

inst/browserCode/lib/igv-patched.js

inst/browserCode/lib/igv.min-2.12.6.js

inst/browserCode/makefile

inst/browserCode/src/igvApp.css

inst/browserCode/src/igvApp.js

inst/browserCode/src/igvApp.pre

inst/demos/bamFile.R inst/demos/bedgraph-svg-bug.R inst/demos/ctcfBamEtc.R inst/demos/customGenome.R

inst/demos/demo.svg

inst/demos/gwasDemo.R inst/demos/gwasUrlDemo.R inst/demos/methylationFromAnnotationHub.R inst/demos/pairedEnd.R inst/demos/quantitativeTrackDemo.R inst/demos/stockGenome.R inst/demos/trackClickDemos.R inst/demos/ucscTableBrowser.R inst/demos/vcfDemo.R

inst/extdata/GRCh38.94.NDUFS2.gff3

inst/extdata/GSM749704_hg19_chr19_128M.bam

inst/extdata/GSM749704_hg19_chr19_128M.bam.bai

inst/extdata/GSM749704_hg19_chr19_narrowPeaks_subset.RData

inst/extdata/GSM749704_hg19_chr19_peaks.narrowPeak

inst/extdata/GSM749704_hg19_chr19_subset.RData

inst/extdata/carolin.gwas

inst/extdata/ctcf-gata2/gata2-region-h3k4me3.bw

inst/extdata/ctcf-gata2/gata2-region-hg19.bam

inst/extdata/ctcf-gata2/gata2-region-hg19.bam.bai

inst/extdata/ctcf-gata2/gata2-region-macs2-narrowPeaks.RData

inst/extdata/gm12878_loops.bedpe.gz

inst/extdata/gwas-3k-clean.RData

inst/extdata/gwas-5k.tsv

inst/extdata/gwas/alzheimerSubsetOfGWASCatatalog-29apr2022.RData

inst/extdata/gwas/ampad.eqtl.ndufs2.RData

inst/extdata/gwas/bellenguez.bed

inst/extdata/gwas/bellenguez.gwas

inst/extdata/gwas/carolin.gwas

inst/extdata/gwas/deelan99.gwas

inst/extdata/k562-h3k4me3-gata2.tsv

inst/extdata/mef2c-4kb.vcf

inst/extdata/mm10-sample.bw

inst/extdata/ndufs2-hg38.gff3

inst/extdata/psg1.bam

inst/extdata/psg1.bam.bai

inst/extdata/sarsGenome/README.txt

inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.101.gff3

inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.dna.toplevel.fa

inst/extdata/sarsGenome/Sars_cov_2.ASM985889v3.dna.toplevel.fa.fai

inst/extdata/sixColumn-demo1.bedpe

inst/extdata/tbl.mef2cGWAS.variants.RData

inst/extdata/tbl.with.MotifDbNames.Rdata

inst/extdata/tenColumn-demo2.bedpe

inst/extdata/tumor.bam

inst/extdata/tumor.bam.bai

inst/unitTests/childrensDemo.R inst/unitTests/igvR-vignette.R inst/unitTests/remoteAlignmentTrackDemo.R inst/unitTests/test_Tracks.R inst/unitTests/test_genomeSpec.R inst/unitTests/test_igvR.R inst/unitTests/test_setCustomGenome.R

makefile

misc/journal-article/bioinformatics.txt

misc/serveYourOwnFiles/htmlOnlyExamples/hg38-explicit.html

misc/serveYourOwnFiles/makefile

misc/serveYourOwnFiles/pythonPrerequisites.txt

misc/serveYourOwnFiles/serveStaticGenomeFiles.py

misc/serveYourOwnFiles/static/Pfalciparum3D7/pfalciparum3D7-hosted.html

misc/serveYourOwnFiles/static/Pfalciparum3D7/pfalciparum3D7.html

misc/serveYourOwnFiles/static/rhos/GCF_000012905.2_ASM1290v2_genomic.fna

misc/serveYourOwnFiles/static/rhos/GCF_000012905.2_ASM1290v2_genomic.fna.fai

misc/serveYourOwnFiles/static/rhos/GCF_000012905.2_ASM1290v2_genomic.fna.gz

misc/serveYourOwnFiles/static/rhos/GCF_000012905.2_ASM1290v2_genomic.gff.gz

misc/serveYourOwnFiles/static/rhos/GCF_000012905.2_ASM1290v2_genomic.gff.gz.tbi

misc/serveYourOwnFiles/static/rhos/rhodobacter-sphaeroides-demo.html

misc/serveYourOwnFiles/static/rhos/test.txt

misc/serveYourOwnFiles/testZeaMaysFromMinnesota/hg38-trackHub-demo.html

misc/serveYourOwnFiles/testZeaMaysFromMinnesota/maize.html

vignettes/ctcf-chip-seq-gata2-252kb-igvR.png

vignettes/igvR-basicDemo.png

vignettes/igvR-ctcf-vignette-zoomedIn.png

vignettes/igvR-ctcf-vignette-zoomedOut.png

vignettes/igvR-ctcf-vignette.png

vignettes/igvR-mef2c-Alzheimers-demo-zoomedIn.png

vignettes/igvR-mef2c-Alzheimers-demo-zoomedOut.png

vignettes/igvR-mef2c-Alzheimers-demo.png

vignettes/images/annotationHub-01.png

vignettes/images/annotationHub-02.png

vignettes/images/ctcfBam-01.png

vignettes/images/ctcfBam-02.png

vignettes/images/ctcfBam-03.png

vignettes/images/ctcfBam-04.png

vignettes/images/ctcfBam-05.png

vignettes/images/ctcfBam-06.png

vignettes/images/ctcfBam-07.png

vignettes/images/ctcfMotif.png

vignettes/images/gata2-63kb-h3k4me3.png

vignettes/images/gata2-63kb.png

vignettes/images/gwas-01.png

vignettes/images/gwas-02.png

vignettes/images/gwas-03.png

vignettes/images/gwas-04.png

vignettes/images/ucscTableBrowser-getOutput.png

vignettes/images/ucscTableBrowser.png

vignettes/images/ucscTableBrowserOutput.png

vignettes/nck2-bedpe.png

vignettes/pairedEnd.R

vignettes/pairedEnd.png

vignettes/stockGenomes.png

vignettes/v00.basicIntro.Rmd vignettes/v01.stockGenome.Rmd vignettes/v02.customGenome.Rmd vignettes/v03.ctcfChIP.Rmd vignettes/v04.pairedEnd.Rmd vignettes/v05.ucscTableBrowser.Rmd vignettes/v06.annotationHub.Rmd vignettes/v07.gwas.Rmd

paul-shannon/IGV documentation built on Nov. 17, 2024, 11:55 p.m.

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paul-shannon/IGV
igvR: integrative genomics viewer

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igvR: integrative genomics viewer

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paul-shannon/IGV igvR: integrative genomics viewer

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R Package Documentation

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paul-shannon/IGV
igvR: integrative genomics viewer

Files in paul-shannon/IGV
igvR: integrative genomics viewer