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  "Type": "Package",
  "Title": "Calculating Linkage Disequilibrium (LD) in Human Population\nGroups of Interest",
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  "Authors@R": "c(person(given = \"Timothy A.\",\nfamily = \"Myers\",\nrole = c(\"aut\", \"cre\"),\nemail = \"myersta@mail.nih.gov\",\ncomment = c(ORCID = \"0000-0001-8127-3446\")),\nperson(given = \"Stephen J.\",\nfamily = \"Chanock\",\nrole = \"aut\",\nemail = \"chanocks@mail.nih.gov\"),\nperson(given = \"Mitchell J.\",\nfamily = \"Machiela\",\nrole = \"aut\",\nemail = \"mitchell.machiela@nih.gov\",\ncomment = c(ORCID = \"0000-0001-6538-9705\")))",
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  "Description": "Provides access to the 'LDlink' API\n(<https://ldlink.nih.gov/?tab=apiaccess>) using the R console.\nThis programmatic access facilitates researchers who are\ninterested in performing batch queries in 1000 Genomes Project\n(2015) <doi:10.1038/nature15393> data using 'LDlink'. 'LDlink'\nis an interactive and powerful suite of web-based tools for\nquerying germline variants in human population groups of\ninterest. For more details, please see Machiela et al. (2015)\n<doi:10.1093/bioinformatics/btv402>.",
  "License": "GPL (>= 2)",
  "URL": "https://ldlink.nih.gov",
  "BugReports": "https://github.com/CBIIT/LDlinkR/issues",
  "Encoding": "UTF-8",
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  "Language": "en-US",
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  "Repository": "https://cbiit.r-universe.dev",
  "Date/Publication": "2024-04-17 13:10:22 UTC",
  "RemoteUrl": "https://github.com/cbiit/ldlinkr",
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  "_topics": [
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    "ldlink",
    "ldlink-api",
    "ldlink-webtool",
    "linkage-disequilibrium",
    "population-genetics"
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    "name": "Center for Biomedical Informatics and Information Technology (CBIIT)"
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  "_realowner": "cbiit",
  "_cranurl": true,
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      "date": "2019-08-01"
    },
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      "version": "1.0.1",
      "date": "2019-10-17"
    },
    {
      "version": "1.0.2",
      "date": "2020-03-02"
    },
    {
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      "date": "2021-02-02"
    },
    {
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      "date": "2021-02-19"
    },
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    },
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    },
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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.",
      "topics": [
        "list_chips"
      ]
    },
    {
      "page": "list_gtex_tissues",
      "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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  "_pkglogo": "https://github.com/cbiit/ldlinkr/raw/HEAD/man/figures/logo.png",
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      "source": "LDlinkR.Rmd",
      "filename": "LDlinkR.html",
      "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",
      "headings": [
        "Introduction",
        "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",
        "list_chips",
        "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",
      "commits": 39
    }
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