Package: INTACT
Type: Package
Title: Integrate TWAS and Colocalization Analysis for Gene Set
        Enrichment Analysis
Version: 1.9.0
Authors@R: c(person("Jeffrey Okamoto", role = c("aut", "cre"),
                     email = "jokamoto@umich.edu",
                     comment=c(ORCID = "0000-0001-9988-1618")),
             person("Xiaoquan Wen", role = c("aut"),
                     email = "xwen@umich.edu",
                     comment=c(ORCID = "0000-0001-8990-2737")))
Description: This package integrates colocalization probabilities from 
    colocalization analysis with transcriptome-wide association study (TWAS)
    scan summary statistics to implicate genes that may be biologically relevant 
    to a complex trait. The probabilistic framework implemented in this package 
    constrains the TWAS scan z-score-based likelihood using a gene-level 
    colocalization probability. Given gene set annotations, this package can 
    estimate gene set enrichment using posterior probabilities from the 
    TWAS-colocalization integration step. 
Depends: R (>= 4.3.0)
Imports: SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2
License: GPL-3 + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Suggests: BiocStyle, knitr, rmarkdown, testthat
BugReports: https://github.com/jokamoto97/INTACT/issues
URL: https://github.com/jokamoto97/INTACT
biocViews: Bayesian, GeneSetEnrichment
LazyData: false
Config/testthat/edition: 3
git_url: https://git.bioconductor.org/packages/INTACT
git_branch: devel
git_last_commit: f08b8a6
git_last_commit_date: 2025-04-15
Repository: Bioconductor 3.22
Date/Publication: 2025-06-04
NeedsCompilation: no
Packaged: 2025-06-04 23:47:35 UTC; biocbuild
Author: Jeffrey Okamoto [aut, cre] (ORCID:
    <https://orcid.org/0000-0001-9988-1618>),
  Xiaoquan Wen [aut] (ORCID: <https://orcid.org/0000-0001-8990-2737>)
Maintainer: Jeffrey Okamoto <jokamoto@umich.edu>
Built: R 4.5.0; ; 2025-06-05 13:13:14 UTC; windows
