Package: INTACT
Type: Package
Title: Integrate TWAS and Colocalization Analysis for Gene Set
        Enrichment Analysis
Version: 1.11.0
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
Config/pak/sysreqs: libicu-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:20:42 UTC
RemoteUrl: https://github.com/bioc/INTACT
RemoteRef: HEAD
RemoteSha: 1b812db34f62b80903490142315994c5c0b6f8e2
NeedsCompilation: no
Packaged: 2026-02-01 08:23:40 UTC; root
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 4.6.0; ; 2026-02-01 08:25:07 UTC; unix
