colocboost

1.0.9

Multi-Context Colocalization Analysis for QTL and GWAS Studies

0packages depend

3.5Kdownloads / year

85.5%test coverage

13/13checks pass

Overview

About

Maintained by Xuewei CaoFirst published 2025-05-026 releasesCRAN page ↗GitHub ↗

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.

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("colocboost", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("StatFunGen/colocboost")

Development version from StatFunGen/colocboost. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-colocboost

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-colocboost

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-colocboost

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 10.4 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.66

85.5%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
11 OK · 0 NOTE · 0 WARNING · 2 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.5K

CRAN downloads in the past year

Rank #11,933 · ~10/day · ~293/mo

Releases R versions

Daily download trend is not available in this view yet.

32330 days

85890 days

3.5K1 year

Compare downloads with other packages →

Also on273 r2u1 autocran

Repository

GitHub ↗ statfungen/colocboost

16Stars

4Forks

1Open issues

0Open PRs

12Releases

587Commits

6Contributors

587 commits · Last activity 2026-07-06 · +6.7% stars, 30d

Stars over time

2025-06-22 · 42026-07-25 · 16

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/statfungen/colocboost on 2026-07-30.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Automation and maintenance (1)

Dependabot

Coverage (1)

.covrignore

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

7 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0.0

Imports (2)

Rfast matrixStats

LinkingTo (0)

none

Suggests (6)

testthat knitr rmarkdown ashrMASSsusieR

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (6)

Maintainer (1)

Xuewei Cao

Maintainer, Author, Copyright holder

Authors (6)

Xuewei Cao

Maintainer, Author, Copyright holder

Kushal Dey

Author, Copyright holder

Ru Feng

Author, Copyright holder

Daniel Nachun

Author, Copyright holder

Haochen Sun

Author, Copyright holder

Gao Wang

Author, Copyright holder

Xuewei Cao

Maintainer, Author, Copyright holder

Kushal Dey

Author, Copyright holder

Ru Feng

Author, Copyright holder

Daniel Nachun

Author, Copyright holder

Haochen Sun

Author, Copyright holder

Gao Wang

Author, Copyright holder

Package Timeline

6 releases. Pick two to compare their code metrics. R releases are shown for context.

1.0.9Latest
2026-06-08 · current release · diff ↗
1.0.8
2026-06-07 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.0.7
2025-11-22 · diff ↗
1.0.6
2025-09-10 · diff ↗
1.0.5
2025-09-08 · diff ↗
1.0.4
2025-05-02
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-02
Total releases: 6 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.0.0
Bundled data: 2.7 MB / 6 files
Download size: 4.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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