https://github.com/iwhalen/tblup
Trait BLUP, a Feature Selection Package for Genomic Prediction
https://github.com/iwhalen/tblup
differential-evolution evolutionary-computation feature-selection genomic-prediction
Last synced: 29 days ago
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Trait BLUP, a Feature Selection Package for Genomic Prediction
- Host: GitHub
- URL: https://github.com/iwhalen/tblup
- Owner: iwhalen
- Created: 2018-05-07T13:09:00.000Z (about 8 years ago)
- Default Branch: master
- Last Pushed: 2018-11-14T00:39:10.000Z (over 7 years ago)
- Last Synced: 2025-11-29T22:40:00.512Z (7 months ago)
- Topics: differential-evolution, evolutionary-computation, feature-selection, genomic-prediction
- Language: Python
- Size: 228 KB
- Stars: 11
- Watchers: 0
- Forks: 3
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# TBLUP
Trait BLUP [1,2], a large scale feature selection for genomic prediction using differential evolution; a fairly simple algorithm that assigns fitness based off an individual's GBLUP [3] accuracy.
See `main.py` for an example of how to run. This implementation uses numpy matrices throughout.
Convert data accordingly.
See `requirements.txt` for dependencies. Use the command `pip3 install -r requirements.txt` to install the required libraries.
See `generate_sbs.py` to generate SLURM sbatch scripts for various experiments.
#### Citations
[1] Esquivelzeta-Rabell, C & Al-Mamun, Hawlader & Lee, Sang-Han & K Lee, H & D Song,
K & Gondro, Cedric. (2015). Evolving to the Best SNP Panel for Hanwoo Breed
Proportion Estimates.
[2] Al-Mamun, Hawlader & Kwan, Paul & Clark, Sam & Lee, Sang-Han & Lee,
H K & Gondro, Cedric. (2015). Genomic Best Linear Unbiased Prediction Using
Differential Evolution.
[3] Clark S.A., van der Werf J. (2013) Genomic Best Linear Unbiased Prediction (gBLUP) for the
Estimation of Genomic Breeding Values. In: Gondro C., van der Werf J., Hayes B. (eds)
Genome-Wide Association Studies and Genomic Prediction. Methods in Molecular Biology (Methods
and Protocols), vol 1019. Humana Press, Totowa, NJ