{
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  "Package": "chimeraviz",
  "Type": "Package",
  "Title": "Visualization tools for gene fusions",
  "Version": "1.39.0",
  "Authors@R": "c(\nperson(\ngiven = \"Stian\",\nfamily = \"Lågstad\",\nemail = \"stianlagstad@gmail.com\",\nrole = c(\"aut\", \"cre\")),\nperson(\ngiven = \"Sen\",\nfamily = \"Zhao\",\nemail = \"Sen.Zhao@rr-research.no\",\nrole = \"ctb\"),\nperson(\ngiven = \"Andreas M.\",\nfamily = \"Hoff\",\nemail = \"andreas.m.hoff@rr-research.no\",\nrole = \"ctb\"),\nperson(\ngiven = \"Bjarne\",\nfamily = \"Johannessen\",\nemail = \"Bjarne.Johannessen@rr-research.no\",\nrole = \"ctb\"),\nperson(\ngiven = \"Ole Christian\",\nfamily = \"Lingjærde\",\nemail = \"ole@ifi.uio.no\",\nrole = \"ctb\"),\nperson(\ngiven = \"Rolf\",\nfamily = \"Skotheim\",\nemail = \"Rolf.I.Skotheim@rr-research.no\",\nrole = \"ctb\"))",
  "Description": "chimeraviz manages data from fusion gene finders and\nprovides useful visualization tools.",
  "License": "Artistic-2.0",
  "SystemRequirements": "bowtie, samtools, and egrep are required for some\nfunctionalities",
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  "URL": "https://github.com/stianlagstad/chimeraviz",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:44:46 UTC",
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  "Author": "Stian Lågstad [aut, cre],\nSen Zhao [ctb],\nAndreas M. Hoff [ctb],\nBjarne Johannessen [ctb],\nOle Christian Lingjærde [ctb],\nRolf Skotheim [ctb]",
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  "_exports": [
    "add_fusion_reads_alignment",
    "create_fusion_report",
    "decide_transcript_category",
    "down_shift",
    "downstream_partner_gene",
    "downstream_partner_gene<-",
    "fetch_reads_from_fastq",
    "fusion_spanning_reads_count",
    "fusion_split_reads_count",
    "fusion_to_data_frame",
    "get_ensembl_ids",
    "get_fusion_by_chromosome",
    "get_fusion_by_gene_name",
    "get_fusion_by_id",
    "get_transcripts_ensembl_db",
    "import_aeron",
    "import_chimpipe",
    "import_defuse",
    "import_ericscript",
    "import_fusioncatcher",
    "import_fusionmap",
    "import_infusion",
    "import_jaffa",
    "import_oncofuse",
    "import_prada",
    "import_soapfuse",
    "import_squid",
    "import_starfusion",
    "partner_gene_ensembl_id",
    "partner_gene_ensembl_id<-",
    "partner_gene_junction_sequence",
    "plot_circle",
    "plot_fusion",
    "plot_fusion_reads",
    "plot_fusion_separate",
    "plot_fusion_together",
    "plot_fusion_transcript",
    "plot_fusion_transcript_with_protein_domain",
    "plot_fusion_transcripts_graph",
    "plot_transcripts",
    "select_transcript",
    "split_on_utr_and_add_feature",
    "upstream_partner_gene",
    "upstream_partner_gene<-",
    "write_fusion_reference"
  ],
  "_help": [
    {
      "page": "add_fusion_reads_alignment",
      "title": "Add fusion reads alignment to fusion object",
      "topics": [
        "add_fusion_reads_alignment"
      ]
    },
    {
      "page": "chimeraviz",
      "title": "chimeraviz: A package for working with and visualizing fusion genes.",
      "topics": [
        "chimeraviz"
      ]
    },
    {
      "page": "chimeraviz-internals-fusions_to_gene_label_data",
      "title": "Create gene label data for RCircos from the given fusions.",
      "topics": [
        ".fusions_to_gene_label_data",
        "chimeraviz-internals-fusions_to_gene_label_data"
      ]
    },
    {
      "page": "chimeraviz-internals-fusions_to_link_data",
      "title": "Create link data for RCircos from the given fusions.",
      "topics": [
        ".fusions_to_link_data",
        "chimeraviz-internals-fusions_to_link_data"
      ]
    },
    {
      "page": "chimeraviz-internals-scaleListToInterval",
      "title": "Scale a vector of numeric values to an interval.",
      "topics": [
        ".scale_list_to_interval",
        "chimeraviz-internals-scaleListToInterval"
      ]
    },
    {
      "page": "create_fusion_report",
      "title": "Create a Fusion Report",
      "topics": [
        "create_fusion_report"
      ]
    },
    {
      "page": "decide_transcript_category",
      "title": "Retrieves transcripts for partner genes in a Fusion object using Ensembldb",
      "topics": [
        "decide_transcript_category"
      ]
    },
    {
      "page": "down_shift",
      "title": "Remove introns and shift exons leftward",
      "topics": [
        "down_shift"
      ]
    },
    {
      "page": "downstream_partner_gene",
      "title": "Get the downstream fusion partner gene",
      "topics": [
        "downstream_partner_gene",
        "downstream_partner_gene,Fusion-method",
        "downstream_partner_gene<-",
        "downstream_partner_gene<-,Fusion-method"
      ]
    },
    {
      "page": "fetch_reads_from_fastq",
      "title": "Fetch reads from fastq files",
      "topics": [
        "fetch_reads_from_fastq"
      ]
    },
    {
      "page": "fusion_spanning_reads_count",
      "title": "Get the spanning reads count from a Fusion object",
      "topics": [
        "fusion_spanning_reads_count",
        "fusion_spanning_reads_count,Fusion-method"
      ]
    },
    {
      "page": "fusion_split_reads_count",
      "title": "Get the split reads count from a Fusion object",
      "topics": [
        "fusion_split_reads_count",
        "fusion_split_reads_count,Fusion-method"
      ]
    },
    {
      "page": "fusion_to_data_frame",
      "title": "Coerce Fusion object to data.frame",
      "topics": [
        "fusion_to_data_frame"
      ]
    },
    {
      "page": "Fusion-class",
      "title": "An S4 class to represent a fusion event.",
      "topics": [
        "Fusion",
        "Fusion-class"
      ]
    },
    {
      "page": "get_ensembl_ids",
      "title": "Get ensembl ids for a fusion object",
      "topics": [
        "get_ensembl_ids"
      ]
    },
    {
      "page": "get_fusion_by_chromosome",
      "title": "Find fusions that involves genes in the given chromosome.",
      "topics": [
        "get_fusion_by_chromosome"
      ]
    },
    {
      "page": "get_fusion_by_gene_name",
      "title": "Find fusions that includes the given gene.",
      "topics": [
        "get_fusion_by_gene_name"
      ]
    },
    {
      "page": "get_fusion_by_id",
      "title": "Find a specific fusion object in a list by id",
      "topics": [
        "get_fusion_by_id"
      ]
    },
    {
      "page": "get_transcripts_ensembl_db",
      "title": "Retrieves transcripts for partner genes in a Fusion object using Ensembldb",
      "topics": [
        "get_transcripts_ensembl_db"
      ]
    },
    {
      "page": "import_aeron",
      "title": "Import results from an Aeron run into a list of Fusion objects.",
      "topics": [
        "import_aeron"
      ]
    },
    {
      "page": "import_chimpipe",
      "title": "Import results from a ChimPipe run into a list of Fusion objects.",
      "topics": [
        "import_chimpipe"
      ]
    },
    {
      "page": "import_defuse",
      "title": "Import results from a deFuse run into a list of Fusion objects.",
      "topics": [
        "import_defuse"
      ]
    },
    {
      "page": "import_ericscript",
      "title": "Import results from a EricScript run into a list of Fusion objects.",
      "topics": [
        "import_ericscript"
      ]
    },
    {
      "page": "import_function_non_ucsc",
      "title": "Alternative import function for Gviz::AlignmentsTrack",
      "topics": [
        "import_function_non_ucsc"
      ]
    },
    {
      "page": "import_fusioncatcher",
      "title": "Import results from a Fusioncatcher run into a list of Fusion objects.",
      "topics": [
        "import_fusioncatcher"
      ]
    },
    {
      "page": "import_fusionmap",
      "title": "Import results from a FusionMap run into a list of Fusion objects.",
      "topics": [
        "import_fusionmap"
      ]
    },
    {
      "page": "import_infusion",
      "title": "Import results from an InFusion run into a list of Fusion objects.",
      "topics": [
        "import_infusion"
      ]
    },
    {
      "page": "import_jaffa",
      "title": "Import results from a JAFFA run into a list of Fusion objects.",
      "topics": [
        "import_jaffa"
      ]
    },
    {
      "page": "import_oncofuse",
      "title": "Import results from a oncofuse run into a list of Fusion objects.",
      "topics": [
        "import_oncofuse"
      ]
    },
    {
      "page": "import_prada",
      "title": "Import results from a PRADA run into a list of Fusion objects.",
      "topics": [
        "import_prada"
      ]
    },
    {
      "page": "import_soapfuse",
      "title": "Import results from a SOAPfuse run into a list of Fusion objects.",
      "topics": [
        "import_soapfuse"
      ]
    },
    {
      "page": "import_squid",
      "title": "Import results from a SQUID run into a list of Fusion objects.",
      "topics": [
        "import_squid"
      ]
    },
    {
      "page": "import_starfusion",
      "title": "Import results from a STAR-Fusion run into a list of Fusion objects.",
      "topics": [
        "import_starfusion"
      ]
    },
    {
      "page": "partner_gene_ensembl_id",
      "title": "Get the Ensembl ID from a PartnerGene object",
      "topics": [
        "partner_gene_ensembl_id",
        "partner_gene_ensembl_id,PartnerGene-method",
        "partner_gene_ensembl_id<-",
        "partner_gene_ensembl_id<-,PartnerGene-method"
      ]
    },
    {
      "page": "partner_gene_junction_sequence",
      "title": "Get the junction sequence from a PartnerGene object",
      "topics": [
        "partner_gene_junction_sequence",
        "partner_gene_junction_sequence,PartnerGene-method"
      ]
    },
    {
      "page": "PartnerGene-class",
      "title": "An S4 class to represent a gene partner in a fusion",
      "topics": [
        "PartnerGene",
        "PartnerGene-class"
      ]
    },
    {
      "page": "plot_circle",
      "title": "Create a circle plot of the given fusions.",
      "topics": [
        "plot_circle"
      ]
    },
    {
      "page": "plot_fusion",
      "title": "Plot a fusion event with transcripts, coverage and ideograms.",
      "topics": [
        "plot_fusion",
        "plot_fusion_separate",
        "plot_fusion_together"
      ]
    },
    {
      "page": "plot_fusion_reads",
      "title": "Create a plot of the reads supporting the given fusion.",
      "topics": [
        "plot_fusion_reads"
      ]
    },
    {
      "page": "plot_fusion_transcript",
      "title": "Plot possible fusion transcripts based on annotation.",
      "topics": [
        "plot_fusion_transcript"
      ]
    },
    {
      "page": "plot_fusion_transcript_with_protein_domain",
      "title": "Plot a specific fusion transcript with protein domain annotations",
      "topics": [
        "plot_fusion_transcript_with_protein_domain"
      ]
    },
    {
      "page": "plot_fusion_transcripts_graph",
      "title": "Graph plot of possible fusion transcripts.",
      "topics": [
        "plot_fusion_transcripts_graph"
      ]
    },
    {
      "page": "plot_transcripts",
      "title": "Plot transcripts for each partner gene in a fusion event.",
      "topics": [
        "plot_transcripts"
      ]
    },
    {
      "page": "raw_chimpipe",
      "title": "ChimPipe data",
      "topics": [
        "raw_chimpipe"
      ]
    },
    {
      "page": "raw_cytobandhg19",
      "title": "Cytoband information HG19",
      "topics": [
        "raw_cytobandhg19"
      ]
    },
    {
      "page": "raw_cytobandhg38",
      "title": "Cytoband information HG138",
      "topics": [
        "raw_cytobandhg38"
      ]
    },
    {
      "page": "raw_defuse",
      "title": "deFuse data",
      "topics": [
        "raw_defuse"
      ]
    },
    {
      "page": "raw_ericscript",
      "title": "EricScript data",
      "topics": [
        "raw_ericscript"
      ]
    },
    {
      "page": "raw_fusion5267proteindomains",
      "title": "protein_domains_5267 bed file",
      "topics": [
        "raw_fusion5267proteindomains"
      ]
    },
    {
      "page": "raw_fusion5267reads",
      "title": "Fusion5267and11759 bamfile",
      "topics": [
        "raw_fusion5267reads"
      ]
    },
    {
      "page": "raw_fusion5267readsBedGraph",
      "title": "Fusion5267and11759 bedGraph file",
      "topics": [
        "raw_fusion5267readsBedGraph"
      ]
    },
    {
      "page": "raw_fusioncatcher",
      "title": "Fusioncatcher data",
      "topics": [
        "raw_fusioncatcher"
      ]
    },
    {
      "page": "raw_fusionmap",
      "title": "FusionMap data",
      "topics": [
        "raw_fusionmap"
      ]
    },
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