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  "Title": "Local Haplotype Clustering and Visualization",
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  "Description": "A local haplotyping visualization toolbox to capture major\npatterns of co-inheritance between clusters of linked variants,\nwhilst connecting findings to phenotypic and demographic traits\nacross individuals. 'crosshap' enables users to explore and\nunderstand genomic variation across a trait-associated region.\nFor an example of successful local haplotype analysis, see\nMarsh et al. (2022) <doi:10.1007/s00122-022-04045-8>.",
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  "BugReports": "https://github.com/jacobimarsh/crosshap/issues",
  "License": "MIT + file LICENSE",
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  "Repository": "https://bradyajohnston.r-universe.dev",
  "Date/Publication": "2024-11-04 21:55:47 UTC",
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    "description": "🦠 Infectious disease simulation & modelling 🧬 Population genetics 🌱 Crop bioinformatics 💻 Software",
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    "prepare_hap_umap",
    "pseudo_haps",
    "read_LD",
    "read_metadata",
    "read_pheno",
    "read_vcf",
    "run_haplotyping",
    "run_hdbscan_haplotyping",
    "tagphenos"
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      "name": "HapObject",
      "title": "Example Haplotype object",
      "object": "HapObject",
      "class": [
        "list"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    },
    {
      "name": "LD",
      "title": "Example LD matrix",
      "object": "LD",
      "class": [
        "data.frame"
      ],
      "fields": [],
      "rows": 2041,
      "table": true,
      "tojson": true
    },
    {
      "name": "metadata",
      "title": "Example Domestication metadata",
      "object": "metadata",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Ind",
        "Metadata"
      ],
      "rows": 1095,
      "table": true,
      "tojson": true
    },
    {
      "name": "pheno",
      "title": "Example phenotype data",
      "object": "pheno",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [
        "Ind",
        "Pheno"
      ],
      "rows": 985,
      "table": true,
      "tojson": true
    },
    {
      "name": "vcf",
      "title": "Example VCF",
      "object": "vcf",
      "class": [
        "tbl_df",
        "tbl",
        "data.frame"
      ],
      "fields": [],
      "rows": 2041,
      "table": true,
      "tojson": true
    }
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      "page": "arith_mode",
      "title": "Mode utility function",
      "topics": [
        "arith_mode"
      ]
    },
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      "page": "build_bot_halfeyeplot",
      "title": "Bot hap-pheno raincloud plot",
      "topics": [
        "build_bot_halfeyeplot"
      ]
    },
    {
      "page": "build_left_alleleplot",
      "title": "Left SNP-allele plot",
      "topics": [
        "build_left_alleleplot"
      ]
    },
    {
      "page": "build_left_posplot",
      "title": "Left SNP-position plot",
      "topics": [
        "build_left_posplot"
      ]
    },
    {
      "page": "build_mid_dotplot",
      "title": "Middle MG/hap dot plot",
      "topics": [
        "build_mid_dotplot"
      ]
    },
    {
      "page": "build_right_clusterplot",
      "title": "Right intra-cluster linkage plot",
      "topics": [
        "build_right_clusterplot"
      ]
    },
    {
      "page": "build_right_phenoplot",
      "title": "Right SNP-pheno phenoplot",
      "topics": [
        "build_right_phenoplot"
      ]
    },
    {
      "page": "build_summary_tables",
      "title": "Hap/MG summary tables",
      "topics": [
        "build_summary_tables"
      ]
    },
    {
      "page": "build_top_metaplot",
      "title": "Top metadata-hap bar plot",
      "topics": [
        "build_top_metaplot"
      ]
    },
    {
      "page": "clustree_viz",
      "title": "Clustering tree",
      "topics": [
        "clustree_viz"
      ]
    },
    {
      "page": "crosshap_viz",
      "title": "Visualize haplotypes",
      "topics": [
        "crosshap_viz"
      ]
    },
    {
      "page": "HapObject",
      "title": "Example Haplotype object",
      "concept": [
        "data"
      ],
      "topics": [
        "HapObject"
      ]
    },
    {
      "page": "LD",
      "title": "Example LD matrix",
      "concept": [
        "data"
      ],
      "topics": [
        "LD"
      ]
    },
    {
      "page": "mean_na.rm",
      "title": "Mean utility function",
      "topics": [
        "mean_na.rm"
      ]
    },
    {
      "page": "metadata",
      "title": "Example Domestication metadata",
      "concept": [
        "data"
      ],
      "topics": [
        "metadata"
      ]
    },
    {
      "page": "pheno",
      "title": "Example phenotype data",
      "concept": [
        "data"
      ],
      "topics": [
        "pheno"
      ]
    },
    {
      "page": "prepare_hap_umap",
      "title": "UMAP haplotype visualization helper",
      "topics": [
        "prepare_hap_umap"
      ]
    },
    {
      "page": "pseudo_haps",
      "title": "Identify haplotypes from clustered SNPs",
      "topics": [
        "pseudo_haps"
      ]
    },
    {
      "page": "read_LD",
      "title": "Read LD correlation matrix to tibble",
      "topics": [
        "read_LD"
      ]
    },
    {
      "page": "read_metadata",
      "title": "Read metadata to tibble",
      "topics": [
        "read_metadata"
      ]
    },
    {
      "page": "read_pheno",
      "title": "Read phenotype data to tibble",
      "topics": [
        "read_pheno"
      ]
    },
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      "title": "Read VCF to tibble",
      "topics": [
        "read_vcf"
      ]
    },
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      "page": "run_haplotyping",
      "title": "Cluster SNPs and identify haplotypes",
      "topics": [
        "run_haplotyping"
      ]
    },
    {
      "page": "run_hdbscan_haplotyping",
      "title": "Cluster SNPs with HDBSCAN and identify haplotypes",
      "topics": [
        "run_hdbscan_haplotyping"
      ]
    },
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      "page": "tagphenos",
      "title": "Calculate SNP phenotypic associations",
      "topics": [
        "tagphenos"
      ]
    },
    {
      "page": "vcf",
      "title": "Example VCF",
      "concept": [
        "data"
      ],
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        "vcf"
      ]
    }
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