INTACT
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see INTACT.
Integrate TWAS and Colocalization Analysis for Gene Set Enrichment Analysis
Bioconductor version: 3.19
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 umich.edu>
citation("INTACT")):
Installation
To install this package, start R (version "4.4") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("INTACT")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("INTACT")| INTACT: Integrate TWAS and Colocalization Analysis for Gene Set Enrichment | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, GeneSetEnrichment, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | SQUAREM, bdsmatrix, numDeriv, stats, tidyr |
| System Requirements | |
| URL | https://github.com/jokamoto97/INTACT |
| Bug Reports | https://github.com/jokamoto97/INTACT/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | INTACT_1.4.0.tar.gz |
| Windows Binary (x86_64) | INTACT_1.4.0.zip |
| macOS Binary (x86_64) | INTACT_1.4.0.tgz |
| macOS Binary (arm64) | INTACT_1.4.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/INTACT |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/INTACT |
| Bioc Package Browser | https://code.bioconductor.org/browse/INTACT/ |
| Package Short Url | https://bioconductor.org/packages/INTACT/ |
| Package Downloads Report | Download Stats |