Files in Bioconductor-mirror/chimeraviz
Visualization tools for gene fusions

.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/AllClasses.R R/chimeraviz.R R/extdata.R R/getFusionBy.R R/importDefuse.R R/importEricscript.R R/importFusioncatcher.R R/importFusionmap.R R/importInfusion.R R/importJaffa.R R/importPrada.R R/importSoapfuse.R R/importStarfusion.R R/plotCircle.R R/plotFusion.R R/plotFusionReads.R R/plotFusionTranscript.R R/plotFusionTranscriptWithProteinDomain.R R/plotFusionTranscriptsGraph.R R/plotTranscripts.R R/reports.R R/utilities.R README.md
chimeraviz.Rproj
fusion-plot-reduced.png
fusion-plot.png
fusion-reads-plot.png
fusion-transcript-graph-plot.png
fusion-transcript-plot-with-protein-domain-annotations.png
fusion-transcript-plot.png
fusion-transcripts-plot.png
inst/NEWS
inst/extdata/5267readsAligned.bam
inst/extdata/5267readsAligned.bam.bai
inst/extdata/FusionMap_01_TestDataset_InputFastq.FusionReport.txt
inst/extdata/Homo_sapiens.GRCh37.74.sqlite
inst/extdata/Homo_sapiens.GRCh37.74_subset.gtf
inst/extdata/PRADA.acc.fusion.fq.TAF.tsv
inst/extdata/UCSC.HG19.Human.CytoBandIdeogram.txt
inst/extdata/UCSC.HG38.Human.CytoBandIdeogram.txt
inst/extdata/defuse_833ke_results.filtered.tsv
inst/extdata/ericscript_SRR1657556.results.total.tsv
inst/extdata/fusion5267and11759reads.bam
inst/extdata/fusion5267and11759reads.bam.bai
inst/extdata/fusion5267and11759reads.bedGraph
inst/extdata/fusioncatcher_833ke_final-list-candidate-fusion-genes.txt
inst/extdata/infusion_fusions.txt
inst/extdata/jaffa_results.csv
inst/extdata/protein_domains_5267.bed
inst/extdata/reads.1.fq
inst/extdata/reads.2.fq
inst/extdata/reads_supporting_defuse_fusion_5267.1.fq
inst/extdata/reads_supporting_defuse_fusion_5267.2.fq
inst/extdata/soapfuse_833ke_final.Fusion.specific.for.genes
inst/extdata/star-fusion.fusion_candidates.final.abridged.txt
inst/reports/fusionListReport.Rmd inst/scripts/bowtie.R inst/scripts/rsubread.R man/Fusion-class.Rd man/PartnerGene-class.Rd man/addFusionReadsAlignment.Rd man/chimeraviz-internals-fusionsToGeneLabelData.Rd man/chimeraviz-internals-fusionsToLinkData.Rd man/chimeraviz-internals-scaleListToInterval.Rd man/chimeraviz.Rd man/createFusionReport.Rd man/decideTranscriptCategory.Rd man/downShift.Rd man/downstreamPartnerGene.Rd man/fetchReadsFromFastq.Rd man/fusionSpanningReadsCount.Rd man/fusionSplitReadsCount.Rd man/fusionToDataFrame.Rd man/getEnsemblIds.Rd man/getFusionByChromosome.Rd man/getFusionByGeneName.Rd man/getFusionById.Rd man/getTranscriptsEnsembldb.Rd man/importDefuse.Rd man/importEricscript.Rd man/importFunctionNonUCSC.Rd man/importFusioncatcher.Rd man/importFusionmap.Rd man/importInfusion.Rd man/importJaffa.Rd man/importPrada.Rd man/importSoapfuse.Rd man/importStarfusion.Rd man/partnerGeneEnsemblId.Rd man/partnerGeneJunctionSequence.Rd man/plotCircle.Rd man/plotFusion.Rd man/plotFusionReads.Rd man/plotFusionTranscript.Rd man/plotFusionTranscriptWithProteinDomain.Rd man/plotFusionTranscriptsGraph.Rd man/plotTranscripts.Rd man/raw_Homo_sapiens.GRCh37.74.Rd man/raw_cytobandhg19.Rd man/raw_cytobandhg38.Rd man/raw_defuse.Rd man/raw_ericscript.Rd man/raw_fusion5267proteindomains.Rd man/raw_fusion5267reads.Rd man/raw_fusion5267readsBedGraph.Rd man/raw_fusioncatcher.Rd man/raw_fusionmap.Rd man/raw_infusion.Rd man/raw_jaffa.Rd man/raw_prada.Rd man/raw_soapfuse.Rd man/raw_starfusion.Rd man/selectTranscript.Rd man/show-Fusion-method.Rd man/show-PartnerGene-method.Rd man/splitOnUtrAndAddFeature.Rd man/upstreamPartnerGene.Rd man/writeFusionReference.Rd
overview-plot.png
tests/testthat.R tests/testthat/test_createFusionReport.R tests/testthat/test_fusionsToGeneLabelData.R tests/testthat/test_fusionsToLinkData.R tests/testthat/test_getFusionBy.R tests/testthat/test_importDefuse.R tests/testthat/test_importEricscript.R tests/testthat/test_importFusioncatcher.R tests/testthat/test_importFusionmap.R tests/testthat/test_importInfusion.R tests/testthat/test_importJaffa.R tests/testthat/test_importPrada.R tests/testthat/test_importSoapfuse.R tests/testthat/test_importStarfusion.R tests/testthat/test_plotCircle.R tests/testthat/test_plotFusion.R tests/testthat/test_plotFusionReads.R tests/testthat/test_plotFusionTranscript.R tests/testthat/test_plotFusionTranscriptWithProteinDomain.R tests/testthat/test_plotFusionTranscriptsGraph.R tests/testthat/test_plotTranscripts.R tests/testthat/test_scaleListToInterval.R tests/testthat/test_selectTranscript.R tests/testthat/test_utilities.R vignettes/chimeraviz-vignette.Rmd
Bioconductor-mirror/chimeraviz documentation built on June 7, 2017, 2:07 p.m.