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  "Type": "Package",
  "Title": "Integrate TWAS and Colocalization Analysis for Gene Set\nEnrichment Analysis",
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  "Authors@R": "c(person(\"Jeffrey Okamoto\", role = c(\"aut\", \"cre\"),\nemail = \"jokamoto@umich.edu\",\ncomment=c(ORCID = \"0000-0001-9988-1618\")),\nperson(\"Xiaoquan Wen\", role = c(\"aut\"),\nemail = \"xwen@umich.edu\",\ncomment=c(ORCID = \"0000-0001-8990-2737\")))",
  "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.",
  "License": "GPL-3 + file LICENSE",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:59:38 UTC",
  "RemoteUrl": "https://github.com/bioc/INTACT",
  "RemoteRef": "RELEASE_3_23",
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    "User": "root"
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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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  "_published": "2026-05-29T08:52:35.192Z",
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      "table": true,
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  "_help": [
    {
      "page": "dot-bf_em_coloc_pi0",
      "title": "Multi-INTACT EM algorithm fixed-point function.",
      "topics": [
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      ]
    },
    {
      "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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    {
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      "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": [
        ".enrich_res"
      ]
    },
    {
      "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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      "page": "dot-logistic_em_nopseudo",
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    },
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      "title": "Compute Multi-INTACT prior parameter estimates and gene product relevance probabilities.",
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      "title": "INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis",
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        "INTACT-GSE: Gene Set Enrichment Estimation Using INTACT results",
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      "date": "2026-05-29T07:44:18.000Z",
      "commit": "a74cea4b958001fd2c24ff77c515818c38918af8",
      "fileid": "c75dca7850762a424fc39489d1f5f3800fad8ffcace2f1a0c35dc1cf00cedfb1",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/26624760374"
    }
  ]
}