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  "Title": "Integrate TWAS and Colocalization Analysis for Gene Set\nEnrichment Analysis",
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  "Description": "This package integrates colocalization probabilities from\ncolocalization analysis with transcriptome-wide association\nstudy (TWAS) scan summary statistics to implicate genes that\nmay be biologically relevant to a complex trait. The\nprobabilistic framework implemented in this package constrains\nthe TWAS scan z-score-based likelihood using a gene-level\ncolocalization probability. Given gene set annotations, this\npackage can estimate gene set enrichment using posterior\nprobabilities from the TWAS-colocalization integration step.",
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  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-28 12:59:38 UTC",
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  "Author": "Jeffrey Okamoto [aut, cre] (ORCID:\n<https://orcid.org/0000-0001-9988-1618>),\nXiaoquan Wen [aut] (ORCID: <https://orcid.org/0000-0001-8990-2737>)",
  "Maintainer": "Jeffrey Okamoto <jokamoto@umich.edu>",
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  "_created": "2026-07-03T17:31:31.000Z",
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      "table": true,
      "tojson": true
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  "_help": [
    {
      "page": "dot-bf_em_coloc_pi0",
      "title": "Multi-INTACT EM algorithm fixed-point function.",
      "topics": [
        ".bf_em_coloc_pi0"
      ]
    },
    {
      "page": "dot-bf_loglik_coloc",
      "title": "Multi-INTACT EM algorithm log-likelihood function.",
      "topics": [
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    },
    {
      "page": "dot-bf_weighted_sum_coloc",
      "title": "Helper function for EM algorithm to compute weighted sum of Bayes factors.",
      "topics": [
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    {
      "page": "dot-em_est",
      "title": "Compute gene set enrichment estimates.",
      "topics": [
        ".em_est"
      ]
    },
    {
      "page": "dot-enrich_bootstrap_se",
      "title": "Compute bootstrap standard errors for alpha MLEs.",
      "topics": [
        ".enrich_bootstrap_se"
      ]
    },
    {
      "page": "dot-enrich_res",
      "title": "Compute gene set enrichment estimates with standard errors.",
      "topics": [
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      ]
    },
    {
      "page": "dot-logistic_em",
      "title": "A fixed-point mapping for the expectation-maximization algorithm. Used as an argument for fixptfn in the squarem function.",
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        "step"
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      "title": "INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis",
      "author": "Jeffrey Okamoto, Xiaoquan Wen",
      "engine": "knitr::rmarkdown",
      "headings": [
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        "INTACT-GSE: Gene Set Enrichment Estimation Using INTACT results",
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      "version": "1.13.0",
      "date": "2026-07-03T17:32:52.000Z",
      "commit": "05b3bdb6ec60fefd76f290eeeaa77ac2914e0af2",
      "fileid": "https://r2.ropensci.org/f2b44eb9e8ac1f4d91d65e2ea61384d1290c7ca45089ab8ecbf138e730450159",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/28675088242"
    }
  ]
}