A collection of Jupyter notebooks for using OpenMendel packages.
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PLINK binary data input, summary statistics, filtering, and visualization. [ipynb]
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Kinship calculation and comparison. [ipynb]
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Population GWAS. [ipynb]
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Iterative hard thresholding (IHT) for GWAS. [ipynb]
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Heritability estimation. [ipynb]
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GWAS based on linear mixed model. [ipynb]
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SNP-set testing. [ipynb]
If you use OpenMendel analysis packages in your research, please cite the following reference in the resulting publications:
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. OPENMENDEL: a cooperative programming project for statistical genetics. Hum Genet. 2020 Jan;139(1):61-71. doi: 10.1007/s00439-019-02001-z. Epub 2019 Mar 26. PMID: 30915546; PMCID: PMC6763373.
This project has been supported by the National Institutes of Health under awards R01GM053275, R01HG006139, R25GM103774, and 1R25HG011845.