Man pages for chimeraviz
Visualization tools for gene fusions

add_fusion_reads_alignmentAdd fusion reads alignment to fusion object
chimeravizchimeraviz: A package for working with and visualizing fusion...
chimeraviz-internals-fusions_to_gene_label_dataCreate gene label data for RCircos from the given fusions.
chimeraviz-internals-fusions_to_link_dataCreate link data for RCircos from the given fusions.
chimeraviz-internals-scaleListToIntervalScale a vector of numeric values to an interval.
create_fusion_reportCreate a Fusion Report
decide_transcript_categoryRetrieves transcripts for partner genes in a Fusion object...
down_shiftRemove introns and shift exons leftward
downstream_partner_geneGet the downstream fusion partner gene
fetch_reads_from_fastqFetch reads from fastq files
Fusion-classAn S4 class to represent a fusion event.
fusion_spanning_reads_countGet the spanning reads count from a Fusion object
fusion_split_reads_countGet the split reads count from a Fusion object
fusion_to_data_frameCoerce Fusion object to data.frame
get_ensembl_idsGet ensembl ids for a fusion object
get_fusion_by_chromosomeFind fusions that involves genes in the given chromosome.
get_fusion_by_gene_nameFind fusions that includes the given gene.
get_fusion_by_idFind a specific fusion object in a list by id
get_transcripts_ensembl_dbRetrieves transcripts for partner genes in a Fusion object...
import_defuseImport results from a deFuse run into a list of Fusion...
import_ericscriptImport results from a EricScript run into a list of Fusion...
import_function_non_ucscAlternative import function for Gviz::AlignmentsTrack
import_fusioncatcherImport results from a Fusioncatcher run into a list of Fusion...
import_fusionmapImport results from a FusionMap run into a list of Fusion...
import_infusionImport results from an InFusion run into a list of Fusion...
import_jaffaImport results from a JAFFA run into a list of Fusion...
import_pradaImport results from a PRADA run into a list of Fusion...
import_soapfuseImport results from a SOAPfuse run into a list of Fusion...
import_starfusionImport results from a STAR-Fusion run into a list of Fusion...
PartnerGene-classAn S4 class to represent a gene partner in a fusion
partner_gene_ensembl_idGet the Ensembl ID from a PartnerGene object
partner_gene_junction_sequenceGet the junction sequence from a PartnerGene object
plot_circleCreate a circle plot of the given fusions.
plot_fusionPlot a fusion event with transcripts, coverage and ideograms.
plot_fusion_readsCreate a plot of the reads supporting the given fusion.
plot_fusion_transcriptPlot possible fusion transcripts based on annotation.
plot_fusion_transcripts_graphGraph plot of possible fusion transcripts.
plot_fusion_transcript_with_protein_domainPlot a specific fusion transcript with protein domain...
plot_transcriptsPlot 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_infusionInFusion data
raw_jaffaJAFFA data
raw_pradaPRADA data
raw_soapfuseSOAPfuse data
raw_starfusionSTAR-Fusion data
select_transcriptSelect which transcript to use (for plotting) for a...
show-Fusion-methodShow method for the Fusion class.
show-PartnerGene-methodShow method for the PartnerGene class.
split_on_utr_and_add_featureSplit GRanges object based on cds
upstream_partner_geneGet the upstream fusion partner gene
write_fusion_referenceWrite fusion junction sequence to a fasta file
chimeraviz documentation built on May 2, 2018, 2:43 a.m.