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  "Package": "loopQTL",
  "Title": "Anchor-Restricted Loop QTL Mapping from Hi-C",
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  "Authors@R": "c(person(\"Rhie Lab at the University of Southern California\", email = \"rhielab@gmail.com\", role = \"cre\"), person(\"Zexun\", \"Wu\", role = \"aut\", email = \"zexunwu@usc.edu\"))",
  "Description": "Maps chromatin loop QTLs by testing whether genotype at a\nloop's anchors associates with the loop's contact strength\nacross samples. Reads .hic files via strawr, builds an\nexact-coordinate consensus loop set, normalizes contact\nstrength across samples via band-wise quantile normalization in\nthe style of BNBC (implemented on top of preprocessCore), and\nruns anchor-restricted SNP-by-loop regressions with MatrixEQTL.\nIntra-chromosomal loops only; no FDR or lead-SNP selection\n(left to the user).",
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      "title": "Class to store loopQTL input data and analysis results",
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        "cis",
        "cis,loopQTL-method",
        "loopQTL-class",
        "loops",
        "loops,loopQTL-method",
        "metadata",
        "metadata,loopQTL-method",
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      "title": "Annotate loopQTL results with target genes and regulatory peaks",
      "topics": [
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      "title": "Auto-select the number of PCs for covariates",
      "topics": [
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      "topics": [
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      "topics": [
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      "title": "Per-sample boxplot for a single SNP-loop pair",
      "topics": [
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      "title": "Validate inputs and build loopQTL object",
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      "title": "Anchor-restricted association testing",
      "topics": [
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