Man pages for Bioconductor-mirror/chimeraviz
Visualization tools for gene fusions

addFusionReadsAlignmentAdd fusion reads alignment to fusion object
chimeravizchimeraviz: A package for working with and visualizing fusion...
chimeraviz-internals-fusionsToGeneLabelDataCreate gene label data for RCircos from the given fusions.
chimeraviz-internals-fusionsToLinkDataCreate link data for RCircos from the given fusions.
chimeraviz-internals-scaleListToIntervalScale a vector of numeric values to an interval.
createFusionReportCreate a Fusion Report
decideTranscriptCategoryRetrieves transcripts for partner genes in a Fusion object...
downShiftRemove introns and shift exons leftward
downstreamPartnerGeneGet the downstream fusion partner gene
fetchReadsFromFastqFetch reads from fastq files
Fusion-classAn S4 class to represent a fusion event.
fusionSpanningReadsCountGet the spanning reads count from a Fusion object
fusionSplitReadsCountGet the split reads count from a Fusion object
fusionToDataFrameCoerce Fusion object to data.frame
getEnsemblIdsGet ensembl ids for a fusion object
getFusionByChromosomeFind fusions that involves genes in the given chromosome.
getFusionByGeneNameFind fusions that includes the given gene.
getFusionByIdFind a specific fusion object in a list by id
getTranscriptsEnsembldbRetrieves transcripts for partner genes in a Fusion object...
importDefuseImport results from a deFuse run into a list of Fusion...
importEricscriptImport results from a EricScript run into a list of Fusion...
importFunctionNonUCSCAlternative import function for Gviz::AlignmentsTrack
importFusioncatcherImport results from a Fusioncatcher run into a list of Fusion...
importFusionmapImport results from a FusionMap run into a list of Fusion...
importInfusionImport results from an InFusion run into a list of Fusion...
importJaffaImport results from a JAFFA run into a list of Fusion...
importPradaImport results from a PRADA run into a list of Fusion...
importSoapfuseImport results from a SOAPfuse run into a list of Fusion...
importStarfusionImport results from a STAR-Fusion run into a list of Fusion...
PartnerGene-classAn S4 class to represent a gene partner in a fusion
partnerGeneEnsemblIdGet the Ensembl ID from a PartnerGene object
partnerGeneJunctionSequenceGet the junction sequence from a PartnerGene object
plotCircleCreate a circle plot of the given fusions.
plotFusionPlot a fusion event with transcripts, coverage and ideograms.
plotFusionReadsCreate a plot of the reads supporting the given fusion.
plotFusionTranscriptPlot possible fusion transcripts based on annotation.
plotFusionTranscriptsGraphGraph plot of possible fusion transcripts.
plotFusionTranscriptWithProteinDomainPlot a specific fusion transcript with protein domain...
plotTranscriptsPlot transcripts for each partner gene in a fusion event.
raw_cytobandhg19Cytoband information HG19
raw_cytobandhg38Cytoband information HG138
raw_defusedeFuse data
raw_ericscriptEricScript data
raw_fusion5267proteindomainsprotein_domains_5267 bed file
raw_fusion5267readsFusion5267and11759 bamfile
raw_fusion5267readsBedGraphFusion5267and11759 bedGraph file
raw_fusioncatcherFusioncatcher data
raw_fusionmapFusionMap data
raw_Homo_sapiens.GRCh37.74Homo_sapiens.GRCh37.74_subset.gtf
raw_infusionInFusion data
raw_jaffaJAFFA data
raw_pradaPRADA data
raw_soapfuseSOAPfuse data
raw_starfusionSTAR-Fusion data
selectTranscriptSelect which transcript to use (for plotting) for a...
show-Fusion-methodShow method for the Fusion class.
show-PartnerGene-methodShow method for the PartnerGene class.
splitOnUtrAndAddFeatureSplit GRanges object based on cds
upstreamPartnerGeneGet the upstream fusion partner gene
writeFusionReferenceWrite fusion junction sequence to a fasta file
Bioconductor-mirror/chimeraviz documentation built on June 7, 2017, 2:07 p.m.