INTACT
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 (3.24)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
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 | 1.13.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (3.5 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | SQUAREM, bdsmatrix, numDeriv, stats, tidyr, ggplot2 |
| 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_1.13.0.tar.gz |
| Windows Binary (x86_64) | INTACT_1.13.0.zip |
| macOS Binary (big-sur-x86_64) | INTACT_1.13.0.tgz |
| macOS Binary (sonoma-arm64) | INTACT_1.13.0.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 |