Crop Genomic Breeding machine (CropGBM) is a multifunctional program that integrates data preprocessing, population structure analysis, SNP selection, phenotype prediction, and data visualization. Has the following advantages:
- Use LightGBM algorithm to quickly and accurately predict phenotype values and support GPU-accelerated training.
- Supports selection and visualization of SNPs that are strongly related to phenotype.
- Support PCA and t-SNE two dimensionality reduction algorithms to extract SNP information.
- Support Kmeans and OPTICS two clustering algorithms to analyze the sample population structure.
- Plot histograms of heterozygosity rate, deletion rate, and frequency of alleles for genotype data.
CropGBM was developed by Yuetong Xu in 2020.
Please read the tutorial for details!