Science Score: 77.0%
This score indicates how likely this project is to be science-related based on various indicators:
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✓CITATION.cff file
Found CITATION.cff file -
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 3 DOI reference(s) in README -
✓Academic publication links
Links to: ncbi.nlm.nih.gov -
✓Committers with academic emails
4 of 5 committers (80.0%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (15.1%) to scientific vocabulary
Keywords from Contributors
Repository
Basic Info
- Host: GitHub
- Owner: OpenMendel
- License: mit
- Language: Julia
- Default Branch: main
- Size: 4.08 MB
Statistics
- Stars: 14
- Watchers: 5
- Forks: 1
- Open Issues: 15
- Releases: 20
Metadata Files
README.md
TrajGWAS
TrajGWAS.jl is a Julia package for performing genome-wide association studies (GWAS) for continuous longitudinal phenotypes using a modified linear mixed effects model. It builds upon the within-subject variance estimation by robust regression (WiSER) method and can be used to identify variants associated with changes in the mean and within-subject variability of the longitduinal trait. The estimation procedure is robust to distributional misspecifications of both the random effects and the response. A saddlepoint approximation (SPA) option is implemented to provide improved power and calibrated type I error for rare variants. It runs efficiently and scales well to very large datasets. The package currently supports PLINK, VCF (both dosage and genotype data), and BGEN file formats. We plan to add PGEN support in the future.
TrajGWAS.jl supports Julia v1.6 or later. See the documentation for usage.
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TrajGWAS.jl is a registered package, and it will require running the following code to install.
{julia}
using Pkg
pkg"add TrajGWAS"
Citation
The methods and applications of this software package are detailed in the following publication:
Ko S, German CA, Jensen A, Shen J, Wang A, Mehrotra DV, Sun YV, Sinsheimer JS, Zhou H, Zhou JJ. GWAS of longitudinal trajectories at biobank scale. Am J Hum Genet. 2022 Mar 3;109(3):433-445. doi: 10.1016/j.ajhg.2022.01.018. Epub 2022 Feb 22. PMID: 35196515; PMCID: PMC8948167.
If you use OpenMendel analysis packages in your research, please cite the following reference in the resulting publications:
OPENMENDEL: a cooperative programming project for statistical genetics. Zhou H, Sinsheimer JS, Bates DM, Chu BB, German CA, Ji SS, Keys KL, Kim J, Ko S, Mosher GD, Papp JC, Sobel EM, Zhai J, Zhou JJ, Lange K. Hum Genet. 139, 61–71 (2020). doi:10.1007/s00439-019-02001-z. PMCID:PMC6763373.
Acknowledgments
This project has been supported by the National Institutes of Health under awards R01GM053275, R01HG006139, R25GM103774, and 1R25HG011845.
Owner
- Name: OpenMendel
- Login: OpenMendel
- Kind: organization
- Repositories: 26
- Profile: https://github.com/OpenMendel
Modern Statistical Genetics Software
Citation (CITATIONS.bib)
@article{ko2022gwas,
title={GWAS of longitudinal trajectories at biobank scale},
author={Ko, Seyoon and German, Christopher A and Jensen, Aubrey and Shen, Judong and Wang, Anran and Mehrotra, Devan V and Sun, Yan V and Sinsheimer, Janet S and Zhou, Hua and Zhou, Jin J},
journal={The American Journal of Human Genetics},
year={2022},
volume={109}
number={3},
pages={433--445},
publisher={Elsevier}
}
GitHub Events
Total
- Create event: 2
- Commit comment event: 4
- Release event: 1
- Issues event: 5
- Watch event: 2
- Issue comment event: 4
- Push event: 281
- Pull request event: 1
Last Year
- Create event: 2
- Commit comment event: 4
- Release event: 1
- Issues event: 5
- Watch event: 2
- Issue comment event: 4
- Push event: 281
- Pull request event: 1
Committers
Last synced: 7 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Seyoon Ko | k****s@u****u | 145 |
| Chris German | g****3@u****u | 27 |
| CompatHelper Julia | c****y@j****g | 5 |
| jcpapp | j****p@m****u | 3 |
| Hua Zhou | h****u@u****u | 3 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 6 months ago
All Time
- Total issues: 20
- Total pull requests: 34
- Average time to close issues: 2 months
- Average time to close pull requests: 2 months
- Total issue authors: 17
- Total pull request authors: 2
- Average comments per issue: 3.55
- Average comments per pull request: 0.21
- Merged pull requests: 11
- Bot issues: 0
- Bot pull requests: 28
Past Year
- Issues: 9
- Pull requests: 1
- Average time to close issues: about 2 months
- Average time to close pull requests: N/A
- Issue authors: 8
- Pull request authors: 1
- Average comments per issue: 1.44
- Average comments per pull request: 0.0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 1
Top Authors
Issue Authors
- zjy71 (2)
- hmtsao (2)
- parekhpravesh (2)
- lis131 (1)
- neurotensin (1)
- Pintaius (1)
- JuliaTagBot (1)
- yunmiji24 (1)
- Buckley96 (1)
- sanniruo (1)
- kose-y (1)
- zqr2008 (1)
- pottj (1)
- RPorneso (1)
- RoyeSie (1)
Pull Request Authors
- github-actions[bot] (30)
- kose-y (6)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
- Total downloads: unknown
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 20
juliahub.com: TrajGWAS
- Documentation: https://docs.juliahub.com/General/TrajGWAS/stable/
- License: MIT
-
Latest release: 0.4.7
published 9 months ago
Rankings
Dependencies
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- julia-actions/julia-buildpkg latest composite
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- julia-actions/setup-julia v1 composite
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