├── .gitignore ├── README.md ├── annotations.sh ├── benjamini.R ├── bonferroni.R ├── broad-scripts ├── README ├── combine_covariates.py ├── normalize_expression.py └── run_PEER.R ├── caviar_full.sh ├── check_beta.R ├── clean_gs.py ├── covariate_correct.py ├── expr_stats.py ├── expression.heatmap.R ├── fastqtl_qvalue.py ├── gcta_full.sh ├── genometricorr.R ├── get_beta.sh ├── get_logp.sh ├── get_pos_samples.py ├── grm.py ├── gt_corr.py ├── gt_error.py ├── gt_to_cn.lumpy.py ├── gt_to_cn.py ├── gtex_row_stats.py ├── impact_rare_shuffle.sh ├── impact_rare_shuffle.var_based.sh ├── impact_score_cdf.py ├── ld.sh ├── ld_continuous.py ├── liftOverBedpe.py ├── lumpy_genome_strip_combine.py ├── mahalanobis.R ├── manhattan_full.sh ├── manhattan_gwas.sh ├── manhattan_plot.R ├── nsamp_limit.sh ├── outlier_enrichment.sh ├── para_sup10_lumpy_scaled.maf.sh ├── para_sup10_lumpy_scaled.sh ├── para_sup10_nonGS_scaled.sh ├── para_sup10_scaled.sh ├── peer.R ├── pheno_samples.py ├── qnorm.py ├── quantile_norm.py ├── rare_var_enrichment.sh ├── row_stats.py ├── run_matrixEQTL.R ├── run_matrixEQTL_for_caviar.R ├── runsvscore ├── generatesvscorecalls.pl ├── runsvscore.sh ├── split.pl ├── split_vcf.py └── vcfanno_8-5-15 │ └── vcfanno ├── scale_gt.py ├── svscore_consolidate.py ├── t-stat.sh ├── var_gt_corr.py ├── vcfToBed.py ├── vcf_allele_freq.py ├── vcf_allele_freq_gs.py ├── vcf_covar.py ├── vcf_svtype.py └── z_norm.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/hall-lab/gtex/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # gtex 2 | -------------------------------------------------------------------------------- /annotations.sh: -------------------------------------------------------------------------------- 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