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  "Title": "Calculating Linkage Disequilibrium (LD) in Human Population\nGroups of Interest",
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  "Date/Publication": "2026-06-22 17:07:51 UTC",
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  "_topics": [
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    "ldlink",
    "ldlink-api",
    "ldlink-webtool",
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  "_realowner": "cbiit",
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      "date": "2019-08-01"
    },
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    },
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      "date": "2020-03-02"
    },
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      "date": "2021-02-02"
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    "LDhap",
    "LDmatrix",
    "LDpair",
    "LDpop",
    "LDproxy",
    "LDproxy_batch",
    "LDtrait",
    "list_chips",
    "list_gtex_tissues",
    "list_pop",
    "SNPchip",
    "SNPclip"
  ],
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    {
      "page": "LDexpress",
      "title": "Determine if genomic variants are associated with gene expression.",
      "topics": [
        "LDexpress"
      ]
    },
    {
      "page": "LDhap",
      "title": "Calculates population specific haplotype frequencies of all haplotypes observed for a list of query variants.",
      "topics": [
        "LDhap"
      ]
    },
    {
      "page": "LDmatrix",
      "title": "Generates a data frame of pairwise linkage disequilibrium statistics.",
      "topics": [
        "LDmatrix"
      ]
    },
    {
      "page": "LDpair",
      "title": "Investigates potentially correlated alleles for a pair of variants.",
      "topics": [
        "LDpair"
      ]
    },
    {
      "page": "LDpop",
      "title": "Investigates allele frequencies and linkage disequilibrium patterns across 1000 Genomes Project populations.",
      "topics": [
        "LDpop"
      ]
    },
    {
      "page": "LDproxy",
      "title": "Explore proxy and putative functional variants for a single query variant.",
      "topics": [
        "LDproxy"
      ]
    },
    {
      "page": "LDproxy_batch",
      "title": "Query LDproxy using a list of query variants, one per line.",
      "topics": [
        "LDproxy_batch"
      ]
    },
    {
      "page": "LDtrait",
      "title": "Determine if genomic variants are associated with a trait or disease.",
      "topics": [
        "LDtrait"
      ]
    },
    {
      "page": "list_chips",
      "title": "Provides a data frame listing the names and abbreviation codes for available commercial SNP Chip Arrays from Illumina and Affymetrix.",
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        "list_chips"
      ]
    },
    {
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      "title": "Provides a data frame listing the GTEx full names, `LDexpress` full names (without spaces) and acceptable abbreviation codes of the 54 non-diseased tissue sites collected for the GTEx Portal and used as input for the `LDexpress` function.",
      "topics": [
        "list_gtex_tissues"
      ]
    },
    {
      "page": "list_pop",
      "title": "Provides a data frame listing the available reference populations from the 1000 Genomes Project.",
      "topics": [
        "list_pop"
      ]
    },
    {
      "page": "SNPchip",
      "title": "Find commercial genotyping chip arrays for variants of interest.",
      "topics": [
        "SNPchip"
      ]
    },
    {
      "page": "SNPclip",
      "title": "Prune a list of variants by linkage disequilibrium.",
      "topics": [
        "SNPclip"
      ]
    }
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      "title": "LDlinkR: An R Package for Rapidly Calculating Linkage Disequilibrium Statistics in Diverse Populations",
      "author": "Timothy A. Myers, Stephen J. Chanock and Mitchell J. Machiela",
      "engine": "knitr::rmarkdown",
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        "Understanding Linkage Disequilibrium",
        "LDlink Data Sources",
        "Calculations",
        "Installation",
        "Personal Access Token - Required",
        "Functions and Examples",
        "LDexpress",
        "Function",
        "Arguments",
        "Usage: Single query variant, multiple populations, multiple tissue types using tissue abbreviation",
        "Usage: Multiple query variants, single population, a tissue type using the full LDexpress tissue name, no spaces, and genome build GRCh38.",
        "LDhap",
        "Usage: Multiple query variants, single population, and genome build GRCh38 High Coverage",
        "Usage: Multiple query variants, multiple populations using default genome build GRCh37 (hg19)",
        "Usage: Multiple query variants, single population, 'merged' output format type.",
        "Usage: Multiple query variants, single population, 'both' output format type.",
        "LDmatrix",
        "Usage: Multiple query variants, single population, R^2^ and genome build GRCh38 (hg38).",
        "Usage: Multiple query variants (mixed use of rsID's & genomic coordinates), multiple populations, D'",
        "Usage: Multiple query variants read from text file, multiple populations, D'",
        "LDpair",
        "Usage: With output argument set to \"text\" and genome build GRCh38 (hg38)",
        "Usage: With no output argument option specified, using default \"table\".",
        "LDpop",
        "Usage",
        "LDproxy",
        "Usage: single reference population and default genome build GRCh37 (hg19).",
        "LDproxy_batch",
        "Usage: multiple variants, default pop and r2d",
        "LDtrait",
        "Usage: Single query variant, multiple reference populations and genome build GRCh38(hg38)",
        "Usage: Multiple query variants, multiple reference populations and win_size set to 750000 base pairs (bp), default genome build GRCh37(hg19).",
        "SNPchip",
        "Usage: Multiple variants, search \"ALL\" available chip arrays",
        "Usage: Multiple variants, search two Affymetrix arrays, and genome build GRCh38 (hg38)",
        "Usage: Multiple variants, search all available Affymetrix arrays using, \"ALL_Affy\"",
        "SNPclip",
        "Usage: Multiple Variants",
        "Utilities and Examples",
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        "list_pop",
        "list_gtex_tissues",
        "FAQs (Frequently Asked Questions)",
        "Session Information"
      ],
      "created": "2021-01-11 19:18:03",
      "modified": "2024-03-04 15:08:10",
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