susieR

0.14.2

Sum of Single Effects Linear Regression

2packages depend

58.2Kdownloads / year

42.6%test coverage

13/13checks pass

Overview

About

Maintained by Peter CarbonettoFirst published 2021-06-0211 releasesCRAN page ↗GitHub ↗

Implements methods for variable selection in linear regression based on the "Sum of Single Effects" (SuSiE) model, as described in Wang et al (2020) DOI:10.1101/501114 and Zou et al (2021) DOI:10.1101/2021.11.03.467167. These methods provide simple summaries, called "Credible Sets", for accurately quantifying uncertainty in which variables should be selected. The methods are motivated by genetic fine-mapping applications, and are particularly well-suited to settings where variables are highly correlated and detectable effects are sparse. The fitting algorithm, a Bayesian analogue of stepwise selection methods called "Iterative Bayesian Stepwise Selection" (IBSS), is simple and fast, allowing the SuSiE model be fit to large data sets (thousands of samples and hundreds of thousands of variables).

Install

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

install.packages("susieR", 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("stephenslab/susieR")

Development version from stephenslab/susieR. 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-susier

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-susieR

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-susieR

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

Health

CRAN checks

13OK

Slowest check: 7.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 0.24

42.6%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-07-16
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-07-09
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 493 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 98%
Return-value docs: 100%
References docs: 22%

Downloads

58.2K

CRAN downloads in the past year

Rank #1,874 · ~159/day · ~4.8K/mo

Releases R versions

Daily download trend is not available in this view yet.

5.7K30 days

13K90 days

58.2K1 year

Compare downloads with other packages →

Also on1.5K r2u35 autocran6.8K conda_forge

Repository

GitHub ↗ stephenslab/susier

264Stars

56Forks

47Open issues

2Open PRs

18Releases

1,839Commits

22Contributors

1,839 commits · Last activity 2026-07-28 · +0.8% stars, 30d

Stars over time

2025-07-30 · 2162026-07-18 · 264

Repository practices

Upstream repositoryBeta

3 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/stephenslab/susier on 2026-07-30.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

Automation and maintenance (1)

Dependabot

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

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (10)

methodsgraphicsgrDevicesstatsMatrixmatrixStats mixsqp reshape crayon ggplot2

LinkingTo (0)

none

Suggests (7)

curl testthat microbenchmark knitr rmarkdown Rfast cowplot

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

3indirect

coloc colocboost

Code & Tests

People & History

People (5)

Maintainer (1)

Peter Carbonetto

Author, Maintainer

Authors (5)

Author, Maintainer

Author

Author

Author

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.14.2Latest
2025-06-05 · current release · diff ↗
0.14.1
2025-06-03 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.12.35
2023-02-17 · diff ↗
0.12.27
2022-09-06 · diff ↗
0.12.19
2022-08-20 · diff ↗
0.12.16
2022-06-27 · diff ↗
0.12.12
2022-06-25 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.11.92
2021-11-12 · diff ↗
0.11.84
2021-11-10 · diff ↗
0.11.42
2021-06-14 · diff ↗
0.11.33
2021-06-02

Show 1 earlier events

R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-06-02
Total releases: 11 / 5 yrs
License: BSD_3_clause + file LICENSE OSI
Minimum R: ≥ 3.0.0
Bundled data: 623 KB / 4 files
Download size: 2.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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