R Observatory: Metrics for coloc version 5.2.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

coloc

5.2.3Package record

Colocalisation Tests of Two Genetic Traits

3packages depend

57Kdownloads / year

14.1%test coverage

13/13flavors OK

Overview

About

Maintained by Chris WallaceCRAN page ↗GitHub ↗Issues ↗

Performs the colocalisation tests described in Giambartolomei et al (2013) doi:10.1371/journal.pgen.1004383, Wallace (2020) doi:10.1371/journal.pgen.1008720, Wallace (2021) doi:10.1371/journal.pgen.1009440.

Changes in 5.2.3

minor change, for another package to be able to access one of the internal functions, it was exported

From NEWS.md in the release

Install

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

install.packages("coloc", 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("chr1swallace/coloc")

Development version from chr1swallace/coloc. 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-coloc

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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

# 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-coloc

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 3.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 5.2.3

READMEYes · 481 wordsVignettesYes · 6 · dynamicNEWSYes · 100% structured · mentions 5.2.3Citation fileYes · cites a publication

Help pages: 39includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 6%
Documented parameters: 99%
Return-value docs: 94%
Help pages citing references: 0%

Vignettes (6)

How these are measured

Downloads

57K

CRAN downloads in the past year

Rank #1,184 · ~156/day · ~4.7K/mo

Releases R versions

Daily download trend is not available in this view yet.

7.3K30 days

28.6K90 days

57K1 year

Compare downloads with other packages →

Also on558 r2u7 autocran8.3K conda_forge1.6K bioconda

How downloads are counted

Repository

chr1swallace/coloc ↗Account: chr1swallace

213Stars

52Forks

67Open issues

2Open PRs

0Releases

366Commits

12Commit identities

366 commits · Last activity 2026-10-16 · +1.9% stars, 30d · Default branch at 6.0.3, ahead of CRAN 5.2.3 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 65%
Median days to close, 50 most recently updated closed issues: 14
Median days to close, 50 most recently updated closed PRs: 1

Stars over time

2025-10-23 · 1772026-10-17 · 213

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 1 family in the upstream repository

Checks run against github.com/chr1swallace/coloc on 2026-10-21.

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-10-16

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing coloc adds 29 packages (14 with compiled code, 29 MB of source tarballs). Heaviest: ggplot2 6.0 MB, data.table 5.7 MB, viridis 2.9 MB.

Depends (1)

R >= 3.5

Imports (8)

data.table ggplot2methodsviridisstatsgrDevicessusieRutils

LinkingTo (0)

none

Suggests (5)

knitr testthat mvtnorm magrittr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

Imports 3

Depends, Imports or LinkingTo, most downloaded first

cophescan RapidoPGS colocPropTest

How these are counted

Code & Tests

Datasets

People & History

People (3)

Chris Wallace

Author, Maintainer since 1.05 (2012)

Claudia Giambartolomei

Author · added in 2.0

Vincent Plagnol

Contributor · added in 2.0

Releases (16)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
5.2.3Latest
record
2023-10-03 · current release · diff ↗ ·
added 2 exports
annotate_susie, process.dataset
5.2.2
record
2023-05-13 · diff ↗ ·
added 3 exports
findends, finemap.bf, subset_dataset
R
R 4.3.0 released · 2023-04-21
5.1.0.1
record
2022-07-05 · diff ↗
R
R 4.2.0 released · 2022-04-22
5.1.0
record
2021-06-14 · diff ↗ ·
removed 8 exports
coloc.abf.datasets, coloc.abf.snpStats, coloc.bma, coloc.test, coloc.test.summary, pcs.model, pcs.prepare, plot

added 12 exports
check.alignment, check.dataset, check_alignment, check_dataset, coloc.bf_bf, coloc.signals, coloc.susie, coloc.susie_bf, finemap.signals, plot_dataset, runsusie, sensitivity
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
3.2-1
record
2019-05-17 · diff ↗
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
3.1
record
2018-02-24 · diff ↗ ·
added 2 exports
finemap.abf, plot
unarchivedReturned to CRAN
2018-02-23

Show 18 earlier eventsHide 18 earlier events

archivedRemoved from CRAN
2018-02-20
check problems were not corrected despite reminders Unconditional use of Suggests package(s) from BioC Different results without long doubles
R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
2.3-1
record
2013-09-29 · diff ↗
2.3
record
2013-09-25 · diff ↗
2.2
record
2013-06-19 · diff ↗ ·
removed 1 export
coloc.abf.imputed
2.1
record
2013-06-03 · diff ↗ ·
added 1 export
coloc.abf.imputed
2.0
record
2013-05-23 · diff ↗ ·
added 4 exports
coloc.abf, coloc.abf.datasets, coloc.abf.snpStats, coloc.test.summary
R
R 3.0.0 released · 2013-04-03
1.11
record
2013-01-25 · diff ↗ ·
added 3 exports
coloc.bma, pcs.model, pcs.prepare
1.10
record
2012-11-30 · diff ↗
1.08
record
2012-04-12 · diff ↗
R
R 2.15.0 released · 2012-03-30
1.07
record
2012-02-22 · diff ↗
1.05
record
2012-01-04
R
R 2.14.0 released · 2011-10-31

Package metadata

First published: 2012-01-04
Total releases: 16 / 14 yrs
License: GPL
Minimum R: ≥ 3.5
Bundled data: 2.1 MB / 2 files
Download size: 3.6 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("coloc")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1371/journal.pgen.1004383, 10.1371/journal.pgen.1008720.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for coloc version 5.2.3 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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