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This is the development version of INTACT; for the stable release version, see INTACT.

Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis

Bioconductor version: Development (3.20)

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.

Author: Jeffrey Okamoto [aut, cre] , Xiaoquan Wen [aut]

Maintainer: Jeffrey Okamoto <jokamoto at>

Citation (from within R, enter citation("INTACT")):


To install this package, start R (version "4.4") and enter:

if (!require("BiocManager", quietly = TRUE))

# The following initializes usage of Bioc devel


For older versions of R, please refer to the appropriate Bioconductor release.


To view documentation for the version of this package installed in your system, start R and enter:

INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment HTML R Script
Reference Manual PDF


biocViews Bayesian, GeneSetEnrichment, Software
Version 1.5.0
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
License GPL-3 + file LICENSE
Depends R (>= 4.3.0)
Imports SQUAREM, bdsmatrix, numDeriv, stats, tidyr
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Source Package INTACT_1.5.0.tar.gz
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