├── .gitignore ├── Analysis ├── README.md ├── example_manhattan_plot.R ├── manhattan_plot.R ├── manplot_1-2.png ├── manplot_2-2.png └── qq_plot.R ├── ExampleData ├── CHR1_GWAS_Zscore.txt.gz ├── CHR1_GWAS_Zscore.txt.gz.tbi ├── CHR1_Pred_GReX.txt ├── CHR1_reference_cov.txt.gz ├── CHR1_reference_cov.txt.gz.tbi ├── PED_Info_MultiPheno.txt ├── PED_Info_SinglePheno.txt ├── README.md ├── eQTLweights.txt ├── eQTLweights.txt.gz ├── eQTLweights.txt.gz.tbi ├── example.vcf.gz ├── example.vcf.gz.tbi ├── example_PED.ped ├── example_PED_binary.ped ├── example_genome_block_CHR1.txt ├── gene_anno.txt ├── gene_exp.txt ├── manplot_TWAS_data.txt ├── sampleID.txt ├── sample_GWAS_Result.txt.gz ├── sample_GWAS_Result.txt.gz.tbi └── test_sampleID.txt ├── Model_Train_Pred ├── DPR ├── DPR_Train.py ├── Elastic_Net_Train.py ├── Prediction.py └── README.md ├── README.md ├── TIGAR_GReX_Pred.sh ├── TIGAR_LD.sh ├── TIGAR_Model_Train.sh ├── TIGAR_TWAS.sh ├── TIGAR_VC_TWAS.sh ├── TIGAR_framework.png ├── TIGARutils.py ├── TWAS ├── Asso_Study_01.py ├── Asso_Study_02.py ├── BGWTWAS_Asso_Study.py ├── Get_LD.py └── README.md ├── VC_TWAS ├── README.md ├── SKAT.py ├── VC_TWAS.py ├── VC_TWAS_summary.py └── qfc_checked.py └── VC_TWAS_summary.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/.gitignore -------------------------------------------------------------------------------- /Analysis/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Analysis/README.md -------------------------------------------------------------------------------- /Analysis/example_manhattan_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Analysis/example_manhattan_plot.R -------------------------------------------------------------------------------- /Analysis/manhattan_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Analysis/manhattan_plot.R -------------------------------------------------------------------------------- /Analysis/manplot_1-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Analysis/manplot_1-2.png -------------------------------------------------------------------------------- /Analysis/manplot_2-2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Analysis/manplot_2-2.png -------------------------------------------------------------------------------- /Analysis/qq_plot.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Analysis/qq_plot.R -------------------------------------------------------------------------------- /ExampleData/CHR1_GWAS_Zscore.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/CHR1_GWAS_Zscore.txt.gz -------------------------------------------------------------------------------- /ExampleData/CHR1_GWAS_Zscore.txt.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/CHR1_GWAS_Zscore.txt.gz.tbi -------------------------------------------------------------------------------- /ExampleData/CHR1_Pred_GReX.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/CHR1_Pred_GReX.txt -------------------------------------------------------------------------------- /ExampleData/CHR1_reference_cov.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/CHR1_reference_cov.txt.gz -------------------------------------------------------------------------------- /ExampleData/CHR1_reference_cov.txt.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/CHR1_reference_cov.txt.gz.tbi -------------------------------------------------------------------------------- /ExampleData/PED_Info_MultiPheno.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/PED_Info_MultiPheno.txt -------------------------------------------------------------------------------- /ExampleData/PED_Info_SinglePheno.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/PED_Info_SinglePheno.txt -------------------------------------------------------------------------------- /ExampleData/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/README.md -------------------------------------------------------------------------------- /ExampleData/eQTLweights.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/eQTLweights.txt -------------------------------------------------------------------------------- /ExampleData/eQTLweights.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/eQTLweights.txt.gz -------------------------------------------------------------------------------- /ExampleData/eQTLweights.txt.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/eQTLweights.txt.gz.tbi -------------------------------------------------------------------------------- /ExampleData/example.vcf.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/example.vcf.gz -------------------------------------------------------------------------------- /ExampleData/example.vcf.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/example.vcf.gz.tbi -------------------------------------------------------------------------------- /ExampleData/example_PED.ped: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/example_PED.ped -------------------------------------------------------------------------------- /ExampleData/example_PED_binary.ped: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/example_PED_binary.ped -------------------------------------------------------------------------------- /ExampleData/example_genome_block_CHR1.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/example_genome_block_CHR1.txt -------------------------------------------------------------------------------- /ExampleData/gene_anno.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/gene_anno.txt -------------------------------------------------------------------------------- /ExampleData/gene_exp.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/gene_exp.txt -------------------------------------------------------------------------------- /ExampleData/manplot_TWAS_data.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/manplot_TWAS_data.txt -------------------------------------------------------------------------------- /ExampleData/sampleID.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/sampleID.txt -------------------------------------------------------------------------------- /ExampleData/sample_GWAS_Result.txt.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/sample_GWAS_Result.txt.gz -------------------------------------------------------------------------------- /ExampleData/sample_GWAS_Result.txt.gz.tbi: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/sample_GWAS_Result.txt.gz.tbi -------------------------------------------------------------------------------- /ExampleData/test_sampleID.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/ExampleData/test_sampleID.txt -------------------------------------------------------------------------------- /Model_Train_Pred/DPR: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Model_Train_Pred/DPR -------------------------------------------------------------------------------- /Model_Train_Pred/DPR_Train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Model_Train_Pred/DPR_Train.py -------------------------------------------------------------------------------- /Model_Train_Pred/Elastic_Net_Train.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Model_Train_Pred/Elastic_Net_Train.py -------------------------------------------------------------------------------- /Model_Train_Pred/Prediction.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Model_Train_Pred/Prediction.py -------------------------------------------------------------------------------- /Model_Train_Pred/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/Model_Train_Pred/README.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/README.md -------------------------------------------------------------------------------- /TIGAR_GReX_Pred.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TIGAR_GReX_Pred.sh -------------------------------------------------------------------------------- /TIGAR_LD.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TIGAR_LD.sh -------------------------------------------------------------------------------- /TIGAR_Model_Train.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TIGAR_Model_Train.sh -------------------------------------------------------------------------------- /TIGAR_TWAS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TIGAR_TWAS.sh -------------------------------------------------------------------------------- /TIGAR_VC_TWAS.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TIGAR_VC_TWAS.sh -------------------------------------------------------------------------------- /TIGAR_framework.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TIGAR_framework.png -------------------------------------------------------------------------------- /TIGARutils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TIGARutils.py -------------------------------------------------------------------------------- /TWAS/Asso_Study_01.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TWAS/Asso_Study_01.py -------------------------------------------------------------------------------- /TWAS/Asso_Study_02.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TWAS/Asso_Study_02.py -------------------------------------------------------------------------------- /TWAS/BGWTWAS_Asso_Study.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TWAS/BGWTWAS_Asso_Study.py -------------------------------------------------------------------------------- /TWAS/Get_LD.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TWAS/Get_LD.py -------------------------------------------------------------------------------- /TWAS/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/TWAS/README.md -------------------------------------------------------------------------------- /VC_TWAS/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/VC_TWAS/README.md -------------------------------------------------------------------------------- /VC_TWAS/SKAT.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/VC_TWAS/SKAT.py -------------------------------------------------------------------------------- /VC_TWAS/VC_TWAS.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/VC_TWAS/VC_TWAS.py -------------------------------------------------------------------------------- /VC_TWAS/VC_TWAS_summary.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/VC_TWAS/VC_TWAS_summary.py -------------------------------------------------------------------------------- /VC_TWAS/qfc_checked.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/VC_TWAS/qfc_checked.py -------------------------------------------------------------------------------- /VC_TWAS_summary.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/yanglab-emory/TIGAR/HEAD/VC_TWAS_summary.sh --------------------------------------------------------------------------------