colocboost: Multi-Context Colocalization Analysis for QTL and GWAS Studies

A multi-task learning approach to variable selection regression with highly correlated predictors and sparse effects, based on frequentist statistical inference. It provides statistical evidence to identify which subsets of predictors have non-zero effects on which subsets of response variables, motivated and designed for colocalization analysis across genome-wide association studies (GWAS) and quantitative trait loci (QTL) studies. The ColocBoost model is described in Cao et. al. (2025) <doi:10.1101/2025.04.17.25326042>.

Version: 1.0.4
Depends: R (≥ 4.0.0)
Imports: Rfast, matrixStats
Suggests: testthat (≥ 3.0.0), knitr, rmarkdown, ashr, MASS, susieR
Published: 2025-05-02
DOI: 10.32614/CRAN.package.colocboost
Author: Xuewei Cao [cre, aut, cph], Haochen Sun [aut, cph], Ru Feng [aut, cph], Daniel Nachun [aut, cph], Kushal Dey [aut, cph], Gao Wang [aut, cph]
Maintainer: Xuewei Cao <xc2270 at cumc.columbia.edu>
BugReports: https://github.com/StatFunGen/colocboost/issues
License: MIT + file LICENSE
URL: https://github.com/StatFunGen/colocboost
NeedsCompilation: no
Citation: colocboost citation info
CRAN checks: colocboost results

Documentation:

Reference manual: colocboost.pdf
Vignettes: Ambiguous Colocalization from Trait-Specific Effects (source, R code)
Animation Example: Proximity Gradient Boosting Algorithm (source, R code)
Bioinformatics Pipeline for ColocBoost (source, R code)
Mixed Data-type and Disease Prioritized Colocalization (source, R code)
Single-trait Fine-mapping with FineBoost (source, R code)
Individual Level Data Colocalization (source, R code)
Input Data Format (source, R code)
Interpret ColocBoost Output (source, R code)
LD mismatch and LD-free Colocalization (source, R code)
Pairwise Colocalization with Flexible Input Formats (source, R code)
Handling partial overlapping variants across traits in ColocBoost (source, R code)
Summary Statistics Data Colocalization (source, R code)
Visualization of ColocBoost Results (source, R code)
News (source)
Installation (source, R code)

Downloads:

Package source: colocboost_1.0.4.tar.gz
Windows binaries: r-devel: colocboost_1.0.4.zip, r-release: colocboost_1.0.4.zip, r-oldrel: colocboost_1.0.4.zip
macOS binaries: r-release (arm64): colocboost_1.0.4.tgz, r-oldrel (arm64): colocboost_1.0.4.tgz, r-release (x86_64): colocboost_1.0.4.tgz, r-oldrel (x86_64): colocboost_1.0.4.tgz

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