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.gitignore
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# Ignore the following directories
Results/
Data/
External_software/
.ipynb_checkpoints/
.vscode/
yeast_RF_results/
yeast_rrBLUP_results/
Scripts/All_Algorithms/
Scripts/Data_Vis/Data_Vis_Figures_64k_geno/
Scripts/Data_Vis/ORF_CNO_Figures/
Scripts/Data_Vis/ORF_CNV_Figures/
Scripts/Data_Vis/SNP_Figures/
Scripts/Data_Vis/Pheno_Figures/
Scripts/Data_Vis/_umap_default/
Scripts/Genomic_Prediction_rrBLUP/rrBLUP_Figures_64k_geno/
Scripts/Genomic_Prediction_RF/RF_64k_geno/
Scripts/Genomic_Prediction_RF/SHAP/ORFs/baseline/
Scripts/Genomic_Prediction_RF/SHAP/ORFs/fs/
Scripts/Genomic_Prediction_XGBoost/XGBoost_Results_64k_geno/
Scripts/Genomic_Prediction_BL/BL_Figures_64k_geno/
Scripts/Genomic_Prediction_GBLUP/GBLUP_64k_geno/
Scripts/Genomic_Prediction_BayesC/BayesC_64k_geno/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr1/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr2/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr3/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr4/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr5/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr6/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr7/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr8/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr9/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr10/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr11/
Scripts/Genomic_Prediction_BayesC/Results_YPDCAFEIN40_chr12/
Scripts/Genomic_Prediction_RKHS/logs
Scripts/Genomic_Prediction_RKHS/output
Scripts/Genomic_Prediction_RKHS/data
Scripts/Genomic_Prediction_GxE/logs
# Files to ignore
Job_Submission_Scripts/SNPs_as_Feat/*.out
Job_Submission_Scripts/SNPs_as_Feat/Feature_Selection/*.out
Job_Submission_Scripts/SNPs_as_Feat/Feature_Selection/rrBLUP/*.out
Job_Submission_Scripts/SNPs_as_Feat/Feature_Selection/BL/*.out
Job_Submission_Scripts/SNPs_as_Feat/Feature_Selection/BayesC/*.out
Job_Submission_Scripts/SNPs_as_Feat/Feature_Selection/XGBoost/*.out
Job_Submission_Scripts/SNPs_as_Feat/RF/rf_PCs_baseline_*
Job_Submission_Scripts/SNPs_as_Feat/RF/*.out
Job_Submission_Scripts/SNPs_as_Feat/BL/*.out
Job_Submission_Scripts/SNPs_as_Feat/Multi-Output_RF/*.out
Job_Submission_Scripts/SNPs_as_Feat/rrBLUP/*.out
Job_Submission_Scripts/SNPs_as_Feat/rrBLUP/rrblup_PCs_3*
Job_Submission_Scripts/ORFs_as_Feat/RF/*.out
Job_Submission_Scripts/ORFs_as_Feat/pheno_training.csv
Job_Submission_Scripts/ORFs_as_Feat/rrBLUP_ORFs_step14_baseline_45359414
Job_Submission_Scripts/ORFs_as_Feat/rrBLUP_ORFs_step9-12_45358058
Job_Submission_Scripts/ORFs_as_Feat/Feature_Selection/RF/*.out
Job_Submission_Scripts/PCs_as_Feat/RF/*.out
Job_Submission_Scripts/Blast_ORFs/*.out
Scripts/Genomic_Prediction_BayesC/*.bin
Scripts/Genomic_Prediction_BayesC/*.dat
Scripts/Genomic_Prediction_BayesC/*.pdf
Scripts/Genomic_Prediction_BayesC/*.csv
Scripts/Genomic_Prediction_BayesC/*.txt
Scripts/Genomic_Prediction_BayesC/BayesC_64k_geno.tar.gz
Scripts/Genomic_Prediction_BayesC/bayesc_12000__*
Scripts/Genomic_Prediction_BayesC/wv_1kb_sliding_*
Scripts/Genomic_Prediction_BL/BL_Figures_64k_geno.tar.gz
Scripts/Genomic_Prediction_GBLUP/BGLR_GBLUP/*.dat
Scripts/Genomic_Prediction_GBLUP/GBLUP_64k_geno.tar.gz
Scripts/Genomic_Prediction_GxE/*.pdf
Scripts/Genomic_Prediction_GxE/*.dat
Scripts/Genomic_Prediction_XGBoost/*.save
Scripts/Genomic_Prediction_XGBoost/*.txt
Scripts/Genomic_Prediction_XGBoost/xgboost_all__*
Scripts/Genomic_Prediction_XGBoost/*.sb
Scripts/Genomic_Prediction_XGBoost/*.out
Scripts/Genomic_Prediction_XGBoost/XGBoost_Results_64k_geno.tar.gz
Scripts/Genomic_Prediction_RF/RF_make_FS_*
Scripts/Genomic_Prediction_RF/*.out
Scripts/Genomic_Prediction_RF/*.csv
Scripts/Genomic_Prediction_RF/*.pdf
Scripts/Genomic_Prediction_RF/*.pkl
Scripts/Genomic_Prediction_RF/*.txt
Scripts/Genomic_Prediction_RF/RF_64k_geno.tar.gz
Scripts/Genomic_Prediction_RF/autopep8_test_Write_FS_script_RF.py
Scripts/Genomic_Prediction_RF/black_test_Write_FS_script_RF.py
Scripts/Genomic_Prediction_RF/yapf_Write_FS_script_RF.py
Scripts/Genomic_Prediction_RF/SHAP/SNPs/fs/*.pdf
Scripts/Genomic_Prediction_RF/SHAP/SNPs/fs/*.csv
Scripts/Genomic_Prediction_RF/SHAP/SNPs/fs/*.tsv
Scripts/Genomic_Prediction_RF/SHAP/SNPs/fs/*.txt
Scripts/Genomic_Prediction_rrBLUP/*.out
Scripts/Genomic_Prediction_rrBLUP/rrBLUP_Figures_64k_geno.tar.gz
Scripts/Data_Vis/*.out
Scripts/Data_Vis/*.csv
Scripts/Data_Vis/*.pdf
Scripts/Data_Vis/*.txt
Scripts/Data_Vis/*.tsv
Scripts/Data_Vis/Data_Vis_Figures_64k_geno.tar.gz
Scripts/Data_Vis/Figures/*.pdf
Scripts/Data_Vis/ORF_CNV_Figures/*.pdf
Scripts/Data_Vis/ORF_CNV_Figures/FS/*.pdf
Scripts/Data_Vis/ORF_CNV_Figures/*.pdf
Scripts/Data_Vis/ORF_CNV_Figures/SHAP_orf_copy_number/*.pdf
Scripts/Data_Vis/ORF_CNV_Figures/SHAP_orf_copy_number/*.tsv
Scripts/Data_Vis/ORF_CNV_Figures/SHAP_orf_presence_absence/*.pdf
Scripts/Data_Vis/ORF_CNV_Figures/SHAP_orf_presence_absence/*.tsv
Results/*.csv
Results/*.pdf
.RData
.Rhistory
Rplots.pdf
Job_Submission_Scripts/Blast_ORFs/ISO1MT_to_peter_orf_tblastx.txt
Job_Submission_Scripts/Blast_ORFs/NC12_to_peter_orf_tblastx.txt
Job_Submission_Scripts/ORFs_as_Feat/Feature_Selection/RF/RF_FS_missing_runs.txt
Job_Submission_Scripts/ORFs_as_Feat/Feature_Selection/RF/RF_FS_runs.txt
Job_Submission_Scripts/ORFs_as_Feat/BayesC/*.out
Job_Submission_Scripts/ORFs_as_Feat/BL/*.out
Job_Submission_Scripts/ORFs_as_Feat/XGBoost/*.out
Job_Submission_Scripts/ORFs_as_Feat/Feature_Selection/BayesC/*.out
Job_Submission_Scripts/ORFs_as_Feat/Feature_Selection/BL/*.out
Job_Submission_Scripts/ORFs_as_Feat/Feature_Selection/rrBLUP/*.out
Job_Submission_Scripts/ORFs_as_Feat/Feature_Selection/XGBoost/*.out
Job_Submission_Scripts/ORFs_as_Feat/rrBLUP/*.out
Job_Submission_Scripts/SNPs_as_Feat/BayesC/*.out
Job_Submission_Scripts/SNPs_as_Feat/PCs_as_Feat/RF/*.out
Job_Submission_Scripts/SNPs_as_Feat/XGBoost/*.out
Job_Submission_Scripts/SNPs_as_Feat/Feature_Selection/RF/*.out
Job_Submission_Scripts/SNPs_as_Feat/Feature_Selection/RF/RF_FS_runs.txt
Job_Submission_Scripts/SNPs_as_Feat/Feature_Selection/RF/RF_FS_missing_runs.txt
Scripts/Data_Processing/*.out
Scripts/Data_Vis/*.png
Scripts/Data_Vis/*.xlsx
Scripts/Data_Vis/Section_1
Scripts/Data_Vis/Section_2
Scripts/Data_Vis/Section_3
Scripts/Data_Vis/Section_4
Scripts/Data_Vis/Section_5
Scripts/Data_Vis/SHAP_Clustering
Scripts/Genomic_Prediction_RF/GO_Enrichment/ORFs_fs
Scripts/Genomic_Prediction_RF/GO_Enrichment/SNPs_fs
Scripts/Genomic_Prediction_RF/PWY_Enrichment/ORFs_fs
Scripts/Genomic_Prediction_RF/PWY_Enrichment/SNPs_fs