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| chimeraviz-package | chimeraviz: A package for working with and visualizing fusion genes. |
| .fusionsToGeneLabelData | Create gene label data for RCircos from the given fusions. |
| .fusionsToLinkData | Create link data for RCircos from the given fusions. |
| .scaleListToInterval | Scale a vector of numeric values to an interval. |
| addFusionReadsAlignment | Add fusion reads alignment to fusion object |
| chimeraviz | chimeraviz: A package for working with and visualizing fusion genes. |
| chimeraviz-internals-fusionsToGeneLabelData | Create gene label data for RCircos from the given fusions. |
| chimeraviz-internals-fusionsToLinkData | Create link data for RCircos from the given fusions. |
| chimeraviz-internals-scaleListToInterval | Scale a vector of numeric values to an interval. |
| createFusionReport | Create a Fusion Report |
| decideTranscriptCategory | Retrieves transcripts for partner genes in a Fusion object using Ensembldb |
| downShift | Remove introns and shift exons leftward |
| downstreamPartnerGene | Get the downstream fusion partner gene |
| downstreamPartnerGene-method | Get the downstream fusion partner gene |
| downstreamPartnerGene<- | Get the downstream fusion partner gene |
| downstreamPartnerGene<--method | Get the downstream fusion partner gene |
| fetchReadsFromFastq | Fetch reads from fastq files |
| Fusion | An S4 class to represent a fusion event. |
| Fusion-class | An S4 class to represent a fusion event. |
| fusionSpanningReadsCount | Get the spanning reads count from a Fusion object |
| fusionSpanningReadsCount-method | Get the spanning reads count from a Fusion object |
| fusionSplitReadsCount | Get the split reads count from a Fusion object |
| fusionSplitReadsCount-method | Get the split reads count from a Fusion object |
| fusionToDataFrame | Coerce Fusion object to data.frame |
| getEnsemblIds | Get ensembl ids for a fusion object |
| getFusionByChromosome | Find fusions that involves genes in the given chromosome. |
| getFusionByGeneName | Find fusions that includes the given gene. |
| getFusionById | Find a specific fusion object in a list by id |
| getTranscriptsEnsembldb | Retrieves transcripts for partner genes in a Fusion object using Ensembldb |
| importDefuse | Import results from a deFuse run into a list of Fusion objects. |
| importEricscript | Import results from a EricScript run into a list of Fusion objects. |
| importFunctionNonUCSC | Alternative import function for Gviz::AlignmentsTrack |
| importFusioncatcher | Import results from a Fusioncatcher run into a list of Fusion objects. |
| importFusionmap | Import results from a FusionMap run into a list of Fusion objects. |
| importInfusion | Import results from an InFusion run into a list of Fusion objects. |
| importJaffa | Import results from a JAFFA run into a list of Fusion objects. |
| importPrada | Import results from a PRADA run into a list of Fusion objects. |
| importSoapfuse | Import results from a SOAPfuse run into a list of Fusion objects. |
| importStarfusion | Import results from a STAR-Fusion run into a list of Fusion objects. |
| PartnerGene | An S4 class to represent a gene partner in a fusion |
| PartnerGene-class | An S4 class to represent a gene partner in a fusion |
| partnerGeneEnsemblId | Get the Ensembl ID from a PartnerGene object |
| partnerGeneEnsemblId-method | Get the Ensembl ID from a PartnerGene object |
| partnerGeneEnsemblId<- | Get the Ensembl ID from a PartnerGene object |
| partnerGeneEnsemblId<--method | Get the Ensembl ID from a PartnerGene object |
| partnerGeneJunctionSequence | Get the junction sequence from a PartnerGene object |
| partnerGeneJunctionSequence-method | Get the junction sequence from a PartnerGene object |
| plotCircle | Create a circle plot of the given fusions. |
| plotFusion | Plot a fusion event with transcripts, coverage and ideograms. |
| plotFusionReads | Create a plot of the reads supporting the given fusion. |
| plotFusionSeparate | Plot a fusion event with transcripts, coverage and ideograms. |
| plotFusionTogether | Plot a fusion event with transcripts, coverage and ideograms. |
| plotFusionTranscript | Plot possible fusion transcripts based on annotation. |
| plotFusionTranscriptsGraph | Graph plot of possible fusion transcripts. |
| plotFusionTranscriptWithProteinDomain | Plot a specific fusion transcript with protein domain annotations |
| plotTranscripts | Plot transcripts for each partner gene in a fusion event. |
| raw_cytobandhg19 | Cytoband information HG19 |
| raw_cytobandhg38 | Cytoband information HG138 |
| raw_defuse | deFuse data |
| raw_ericscript | EricScript data |
| raw_fusion5267proteindomains | protein_domains_5267 bed file |
| raw_fusion5267reads | Fusion5267and11759 bamfile |
| raw_fusion5267readsBedGraph | Fusion5267and11759 bedGraph file |
| raw_fusioncatcher | Fusioncatcher data |
| raw_fusionmap | FusionMap data |
| raw_Homo_sapiens.GRCh37.74 | Homo_sapiens.GRCh37.74_subset.gtf |
| raw_infusion | InFusion data |
| raw_jaffa | JAFFA data |
| raw_prada | PRADA data |
| raw_soapfuse | SOAPfuse data |
| raw_starfusion | STAR-Fusion data |
| selectTranscript | Select which transcript to use (for plotting) for a GenePartner object |
| show-method | Show method for the Fusion class. |
| show-method | Show method for the PartnerGene class. |
| splitOnUtrAndAddFeature | Split GRanges object based on cds |
| upstreamPartnerGene | Get the upstream fusion partner gene |
| upstreamPartnerGene-method | Get the upstream fusion partner gene |
| upstreamPartnerGene<- | Get the upstream fusion partner gene |
| upstreamPartnerGene<--method | Get the upstream fusion partner gene |
| writeFusionReference | Write fusion junction sequence to a fasta file |