trajgwas-reproducibility
Science Score: 44.0%
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
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✓DOI references
Found 3 DOI reference(s) in README -
○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (5.2%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: kose-y
- Language: Jupyter Notebook
- Default Branch: main
- Size: 632 KB
Statistics
- Stars: 1
- Watchers: 4
- Forks: 1
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
TrajGWAS reproducibility
Scripts to reproduce the experiments performed for the TrajGWAS manuscript:
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. The American Journal of Human Genetics. In press. doi:10.1016/j.ajhg.2022.01.018.
simulation
Scripts for reproducing simulation studies. Experiments are conducted with an older version of TrajGWAS, named vGWAS. This version of package is kept on the branch gwas_dev of the package repository. You can load this version following the instruction inside the directory.
ukbiobank
Scripts for UK Biobank data analyses. It can run with TrajGWAS v0.1.2. Its optimization interface has changed to MathOptInterface since v0.4, and KNITRO.KnitroSolver no longer works. Use
julia
solver = KNITRO.Optimizer()
solver_config = Dict("outlev" => 3)
as keyword arguments for the trajgwas() function instead to run with newer version of TrajGWAS and KNITRO.
Owner
- Name: Seyoon Ko
- Login: kose-y
- Kind: user
- Location: Los Angeles
- Company: University of California, Los Angeles
- Website: https://kose-y.github.io
- Repositories: 11
- Profile: https://github.com/kose-y
Postdoc at UCLA Computational Medicine
Citation (CITATION.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={in press},
publisher={Elsevier}
}
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