susieR

R package for "sum of single effects" regression.

https://github.com/stephenslab/susier

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
Found 6 DOI reference(s) in README
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Academic publication links
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Committers with academic emails
4 of 13 committers (30.8%) from academic institutions
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Institutional organization owner
Organization stephenslab has institutional domain (stephenslab.uchicago.edu)
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (16.9%) to scientific vocabulary

Last synced: 6 months ago · JSON representation

Repository

R package for "sum of single effects" regression.

Basic Info

Host: GitHub
Owner: stephenslab
License: other
Language: R
Default Branch: master
Homepage: https://stephenslab.github.io/susieR
Size: 69.4 MB

Statistics

Stars: 220
Watchers: 12
Forks: 53
Open Issues: 89
Releases: 11

Created almost 8 years ago · Last pushed 6 months ago

Metadata Files

Readme License

susieR

The susieR package implements a simple new way to perform variable selection in multiple regression ($y=Xb+e$). The methods implemented here are particularly well-suited to settings where some of the X variables are highly correlated, and the true effects are highly sparse (e.g. <20 non-zero effects in the vector $b$). One example of this is genetic fine-mapping applications, and this application was a major motivation for developing these methods. However, the methods should also be useful more generally.

The methods are based on a new model for sparse multiple regression, which we call the "Sum of Single Effects" (SuSiE) model. This model, which will be described in a manuscript in preparation (Wang et al), lends itself to a particularly simple and intuitive fitting procedure -- effectively a Bayesian modification of simple forward selection, which we call "Iterative Bayesian Step-wise Selection".

The output of the fitting procedure is a number of "Credible Sets" (CSs), which are each designed to have high probability to contain a variable with non-zero effect, while at the same time being as small as possible. You can think of the CSs as being a set of "highly correlated" variables that are each associated with the response: you can be confident that one of the variables has a non-zero coefficient, but they are too correlated to be sure which one.

The package is developed by Gao Wang, Peter Carbonetto, Yuxin Zou, Kaiqian Zhang, and Matthew Stephens from the Stephens Lab at the University of Chicago.

Please post issues to ask questions, get our support or provide us feedback; please send pull requests if you have helped fixing bugs or making improvements to the source code.

Quick Start

Install susieR from CRAN:

R install.packages("susieR")

Alternatively, install the latest development version of susieR from GitHub:

```R

install.packages("remotes")

remotes::install_github("stephenslab/susieR") ```

See here for a brief illustration of susieR. For more documentation and examples please visit https://stephenslab.github.io/susieR

Citing this work

If you find the susieR package or any of the source code in this repository useful for your work, please cite:

G. Wang, G., Sarkar, A., Carbonetto, P. & Stephens, M. (2020). A simple new approach to variable selection in regression, with application to genetic fine mapping. Journal of the Royal Statistical Society, Series B 82, 1273–1300. https://doi.org/10.1111/rssb.12388

If you use any of the summary data methods such as susie_suff_stat or susie_rss, please also cite:

Zou, Y., Carbonetto, P., Wang, G. & Stephens, M. (2022). Fine-mapping from summary data with the "Sum of Single Effects" model. PLoS Genetics 18, e1010299. https://doi.org/10.1371/journal.pgen.1010299

Developer notes

When any changes are made to roxygen2 markup, run devtools::document() to update package NAMESPACE and documentation files.
Run pkgdown::build_site() to build the website. Getting pkgdown to work properly can be frustrating due to numerous & fragile dependencies. If pkgdown does not work for you out of the box you can use this docker command to run all vignettes and build the site:

bash docker run --rm --security-opt label:disable -t -P -w $PWD -v $PWD:$PWD \ -u $UID:${GROUPS[0]} -e HOME=/home/$USER -e USER=$USER gaow/susie \ R --slave -e "pkgdown::build_site(lazy=TRUE, examples=FALSE)"

Owner

Name: Stephens lab
Login: stephenslab
Kind: organization

Website: http://stephenslab.uchicago.edu
Repositories: 95
Profile: https://github.com/stephenslab

Research in statistical and computational methods for genetics at the University of Chicago.

GitHub Events

Total

Issues event: 22
Watch event: 36
Issue comment event: 84
Push event: 22
Pull request event: 7
Fork event: 8
Create event: 1

Last Year

Issues event: 22
Watch event: 36
Issue comment event: 84
Push event: 22
Pull request event: 7
Fork event: 8
Create event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 946
Total Committers: 13
Avg Commits per committer: 72.769
Development Distribution Score (DDS): 0.668

Past Year

Commits: 15
Committers: 1
Avg Commits per committer: 15.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Peter Carbonetto	p**o@g**m	314
Gao Wang	g**w@u**u	227
zouyuxin	y**t@g**m	181
Gao Wang	w**w@g**m	77
stephens999	s**9@g**m	63
KaiqianZhang	z**7@g**u	47
kaiqian	k**z@u**u	24
Yuxin Zou	y**u@r**m	5
John Blischak	j**k@g**m	3
Arya Massarat	2****m	2
Kangcheng Hou	k**u@g**m	1
Chris Wallace	c**4@c**k	1
Nicholas Knoblauch	n**h@g**m	1

Committer Domains (Top 20 + Academic)

uchicago.edu: 2 cam.ac.uk: 1 regeneron.com: 1 grinnell.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 158
Total pull requests: 19
Average time to close issues: 5 months
Average time to close pull requests: 13 days
Total issue authors: 81
Total pull request authors: 10
Average comments per issue: 5.32
Average comments per pull request: 1.42
Merged pull requests: 18
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 18
Pull requests: 10
Average time to close issues: 2 days
Average time to close pull requests: about 16 hours
Issue authors: 14
Pull request authors: 4
Average comments per issue: 1.56
Average comments per pull request: 0.7
Merged pull requests: 9
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

garyzhubc (20)
pcarbo (15)
gaow (11)
katherinef (7)
jerome-f (5)
stephens999 (4)
PhoebeGuo97 (4)
karenfeng (4)
Xi-Cao (3)
koujiaodahan (3)
Huifang-Xu (2)
william-denault (2)
leoarrow1 (2)
tianwen0003 (2)
MoMaz123 (2)

Pull Request Authors

wesleycrouse (4)
william-denault (3)
jdblischak (3)
joshchiou (2)
aksarkar (2)
pcarbo (2)
gaow (1)
chr1swallace (1)
aryarm (1)
KangchengHou (1)

Top Labels

Issue Labels

enhancement (4) bug (1)

Pull Request Labels

Packages

Total packages: 4
Total downloads:
- cran 3,518 last-month
Total docker downloads: 187

Total dependent packages: 1
(may contain duplicates)
Total dependent repositories: 12
(may contain duplicates)
Total versions: 37
Total maintainers: 1

proxy.golang.org: github.com/stephenslab/susieR

Documentation: https://pkg.go.dev/github.com/stephenslab/susieR#section-documentation
License: other
Latest release: v0.14.2
published 9 months ago

Versions: 9
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 6 months ago

proxy.golang.org: github.com/stephenslab/susier

Documentation: https://pkg.go.dev/github.com/stephenslab/susier#section-documentation
License: other
Latest release: v0.14.2
published 9 months ago

Versions: 9
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent packages count: 5.4%

Average: 5.6%

Dependent repos count: 5.8%

Last synced: 6 months ago

cran.r-project.org: susieR

Sum of Single Effects Linear Regression

Homepage: https://github.com/stephenslab/susieR
Documentation: http://cran.r-project.org/web/packages/susieR/susieR.pdf
License: BSD_3_clause + file LICENSE
Latest release: 0.14.2
published 9 months ago

Versions: 11
Dependent Packages: 1
Dependent Repositories: 12
Downloads: 3,518 Last month
Docker Downloads: 187

Rankings

Forks count: 2.2%

Stargazers count: 2.7%

Dependent repos count: 8.3%

Downloads: 11.0%

Average: 11.8%

Dependent packages count: 18.1%

Docker downloads count: 28.1%

Maintainers (1)

peter.carbonetto@gmail.com

Last synced: 6 months ago

conda-forge.org: r-susier

Homepage: https://github.com/stephenslab/susieR
License: MIT
Latest release: 0.12.27
published over 3 years ago

Versions: 8
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Stargazers count: 28.5%

Forks count: 29.9%

Dependent repos count: 34.0%

Average: 35.9%

Dependent packages count: 51.2%

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.0.0 depends
Matrix * imports
crayon * imports
ggplot2 * imports
grDevices * imports
graphics * imports
matrixStats * imports
methods * imports
mixsqp * imports
reshape * imports
stats * imports
L0Learn * suggests
Rfast * suggests
cowplot * suggests
curl * suggests
knitr * suggests
microbenchmark * suggests
rmarkdown * suggests
testthat * suggests

susieR

Science Score: 57.0%

Repository

Basic Info

Statistics

Metadata Files

README.md

susieR

Quick Start

install.packages("remotes")

Citing this work

Developer notes

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

proxy.golang.org: github.com/stephenslab/susieR

Rankings

proxy.golang.org: github.com/stephenslab/susier

Rankings

cran.r-project.org: susieR

Rankings

Maintainers (1)

conda-forge.org: r-susier

Rankings

Dependencies