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  "Package": "NanoMethViz",
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  "Title": "Visualise methylation data from Oxford Nanopore sequencing",
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  "Authors@R": "c(\nperson(\"Shian\", \"Su\", email = \"su.s@wehi.edu.au\", role = c(\"cre\", \"aut\")))",
  "Description": "NanoMethViz is a toolkit for visualising methylation data\nfrom Oxford Nanopore sequencing. It can be used to explore\nmethylation patterns from reads derived from Oxford Nanopore\ndirect DNA sequencing with methylation called by callers\nincluding nanopolish, f5c and megalodon. The plots in this\npackage allow the visualisation of methylation profiles\naggregated over experimental groups and across classes of\ngenomic features.",
  "biocViews": "Software, LongRead, Visualization, DifferentialMethylation,\nDNAMethylation, Epigenetics, DataImport",
  "URL": "https://github.com/shians/NanoMethViz,\nhttps://shians.github.io/NanoMethViz/",
  "BugReports": "https://github.com/Shians/NanoMethViz/issues",
  "License": "Apache License (>= 2.0)",
  "SystemRequirements": "C++20",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:54:18 UTC",
  "RemoteUrl": "https://github.com/bioc/NanoMethViz",
  "RemoteRef": "RELEASE_3_23",
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  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-02 08:46:08 UTC",
    "User": "root"
  },
  "Author": "Shian Su [cre, aut]",
  "Maintainer": "Shian Su <su.s@wehi.edu.au>",
  "MD5sum": "a518cde71c9883d74ca4c5824735a3c3",
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  "_created": "2026-06-02T08:46:08.000Z",
  "_published": "2026-06-02T09:10:46.802Z",
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  "_exports": [
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    "bsseq_to_log_methy_ratio",
    "cluster_regions",
    "create_tabix_file",
    "exons",
    "exons_to_genes",
    "exons<-",
    "filter_methy",
    "get_cgi_grcm39",
    "get_cgi_hg19",
    "get_cgi_hg38",
    "get_cgi_mm10",
    "get_cgi_t2t",
    "get_example_exons_mus_musculus",
    "get_exons_grcm39",
    "get_exons_hg19",
    "get_exons_hg38",
    "get_exons_homo_sapiens",
    "get_exons_mm10",
    "get_exons_mus_musculus",
    "get_exons_t2t",
    "load_example_modbamresult",
    "load_example_nanomethresult",
    "methy",
    "methy_col_names",
    "methy_to_bsseq",
    "methy_to_edger",
    "methy<-",
    "mod_code",
    "mod_code<-",
    "modbam_to_tabix",
    "ModBamFiles",
    "ModBamResult",
    "NanoMethResult",
    "plot_agg_genes",
    "plot_agg_regions",
    "plot_gene",
    "plot_gene_heatmap",
    "plot_grange",
    "plot_grange_heatmap",
    "plot_mds",
    "plot_pca",
    "plot_region",
    "plot_region_heatmap",
    "plot_violin",
    "query_exons_gene_id",
    "query_exons_region",
    "query_exons_symbol",
    "query_methy",
    "region_methy_stats",
    "samples",
    "samples<-",
    "show",
    "sigmoid"
  ],
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      "page": "bsseq_to_edger",
      "title": "Convert BSseq object to edgeR methylation matrix",
      "topics": [
        "bsseq_to_edger"
      ]
    },
    {
      "page": "bsseq_to_log_methy_ratio",
      "title": "Convert BSseq object to log-methylation-ratio matrix",
      "topics": [
        "bsseq_to_log_methy_ratio"
      ]
    },
    {
      "page": "cluster_reads",
      "title": "Cluster reads based on methylation",
      "topics": [
        "cluster_reads"
      ]
    },
    {
      "page": "cluster_regions",
      "title": "Cluster regions by K-means",
      "topics": [
        "cluster_regions"
      ]
    },
    {
      "page": "create_tabix_file",
      "title": "Create a tabix file using methylation calls",
      "topics": [
        "create_tabix_file"
      ]
    },
    {
      "page": "exons_to_genes",
      "title": "Convert exon annotation to genes",
      "topics": [
        "exons_to_genes"
      ]
    },
    {
      "page": "filter_methy",
      "title": "Create filtered methylation file",
      "topics": [
        "filter_methy"
      ]
    },
    {
      "page": "get_exons",
      "title": "Get exon annotations",
      "topics": [
        "get_cgi_grcm39",
        "get_cgi_hg19",
        "get_cgi_hg38",
        "get_cgi_mm10",
        "get_cgi_t2t",
        "get_exons",
        "get_exons_grcm39",
        "get_exons_hg19",
        "get_exons_hg38",
        "get_exons_mm10",
        "get_exons_t2t"
      ]
    },
    {
      "page": "get_example_exons_mus_musculus",
      "title": "Get example exon annotations for mus musculus (mm10)",
      "topics": [
        "get_example_exons_mus_musculus"
      ]
    },
    {
      "page": "get_exons_homo_sapiens",
      "title": "Get exon annotations for Homo sapiens (hg19)",
      "topics": [
        "get_exons_homo_sapiens"
      ]
    },
    {
      "page": "get_exons_mus_musculus",
      "title": "Get exon annotations for Mus musculus (mm10)",
      "topics": [
        "get_exons_mus_musculus"
      ]
    },
    {
      "page": "load_example_modbamresult",
      "title": "Load an example ModBamResult object",
      "topics": [
        "load_example_modbamresult"
      ]
    },
    {
      "page": "load_example_nanomethresult",
      "title": "Load an example NanoMethResult object",
      "topics": [
        "load_example_nanomethresult"
      ]
    },
    {
      "page": "methy_col_names",
      "title": "Column names for methylation data",
      "topics": [
        "methy_col_names"
      ]
    },
    {
      "page": "methy_to_bsseq",
      "title": "Create BSSeq object from methylation tabix file",
      "topics": [
        "methy_to_bsseq"
      ]
    },
    {
      "page": "methy_to_edger",
      "title": "Convert NanoMethResult object to edgeR methylation matrix",
      "topics": [
        "methy_to_edger"
      ]
    },
    {
      "page": "modbam_to_tabix",
      "title": "Convert BAM with modifications to tabix format",
      "topics": [
        "modbam_to_tabix"
      ]
    },
    {
      "page": "ModBamFiles",
      "title": "Constructor for a ModBamFiles object",
      "topics": [
        "ModBamFiles",
        "show,ModBamFiles-method"
      ]
    },
    {
      "page": "ModBamFiles-class",
      "title": "ModBamFiles class",
      "topics": [
        "ModBamFiles-class"
      ]
    },
    {
      "page": "ModBamResult-class",
      "title": "modBAM methylation results",
      "topics": [
        "exons,ModBamResult-method",
        "exons<-,ModBamResult,data.frame-method",
        "methy,ModBamResult-method",
        "methy<-,ModBamResult,ModBamFiles-method",
        "ModBamResult",
        "ModBamResult-class",
        "mod_code,ModBamResult-method",
        "mod_code<-,ModBamResult,character-method",
        "samples,ModBamResult-method",
        "samples<-,ModBamResult,data.frame-method"
      ]
    },
    {
      "page": "NanoMethResult-class",
      "title": "Nanopore Methylation Result",
      "topics": [
        "exons,NanoMethResult-method",
        "exons<-,NanoMethResult,data.frame-method",
        "methy,NanoMethResult-method",
        "methy<-,NanoMethResult,ANY-method",
        "NanoMethResult",
        "NanoMethResult-class",
        "samples,NanoMethResult-method",
        "samples<-,NanoMethResult,data.frame-method"
      ]
    },
    {
      "page": "plot_agg_genes",
      "title": "Plot gene aggregate plot",
      "topics": [
        "plot_agg_genes"
      ]
    },
    {
      "page": "plot_agg_regions",
      "title": "Plot aggregate regions",
      "topics": [
        "plot_agg_regions"
      ]
    },
    {
      "page": "plot_gene",
      "title": "Plot gene methylation",
      "topics": [
        "plot_gene",
        "plot_gene,ModBamResult,character-method",
        "plot_gene,NanoMethResult,character-method"
      ]
    },
    {
      "page": "plot_gene_heatmap",
      "title": "Plot gene methylation heatmap",
      "topics": [
        "plot_gene_heatmap",
        "plot_gene_heatmap,ModBamResult,character-method",
        "plot_gene_heatmap,NanoMethResult,character-method"
      ]
    },
    {
      "page": "plot_grange",
      "title": "Plot GRanges",
      "topics": [
        "plot_grange"
      ]
    },
    {
      "page": "plot_grange_heatmap",
      "title": "Plot GRanges heatmap",
      "topics": [
        "plot_grange_heatmap"
      ]
    },
    {
      "page": "plot_mds",
      "title": "Plot MDS",
      "topics": [
        "plot_mds"
      ]
    },
    {
      "page": "plot_pca",
      "title": "Plot PCA",
      "topics": [
        "plot_pca"
      ]
    },
    {
      "page": "plot_region",
      "title": "Plot region methylation",
      "topics": [
        "plot_region",
        "plot_region,ModBamResult,character,numeric,numeric-method",
        "plot_region,ModBamResult,factor,numeric,numeric-method",
        "plot_region,NanoMethResult,character,numeric,numeric-method",
        "plot_region,NanoMethResult,factor,numeric,numeric-method"
      ]
    },
    {
      "page": "plot_region_heatmap",
      "title": "Plot region methylation heatmap",
      "topics": [
        "plot_region_heatmap",
        "plot_region_heatmap,ModBamResult,character,numeric,numeric-method",
        "plot_region_heatmap,ModBamResult,factor,numeric,numeric-method",
        "plot_region_heatmap,NanoMethResult,character,numeric,numeric-method",
        "plot_region_heatmap,NanoMethResult,factor,numeric,numeric-method"
      ]
    },
    {
      "page": "plot_violin",
      "title": "Plot violin for regions",
      "topics": [
        "plot_violin"
      ]
    },
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