├── .gitignore ├── README.md ├── plots ├── PR │ ├── glasso_canonical_artery.png │ ├── glasso_canonical_blood.png │ ├── glasso_canonical_lung.png │ ├── glasso_canonical_muscle.png │ ├── glasso_canonical_nerve.png │ ├── glasso_canonical_skin.png │ ├── glasso_canonical_subcutaneous.png │ ├── glasso_canonical_thyroid.png │ ├── glasso_shared_artery.png │ ├── glasso_shared_blood.png │ ├── glasso_shared_lung.png │ ├── glasso_shared_muscle.png │ ├── glasso_shared_nerve.png │ ├── glasso_shared_skin.png │ ├── glasso_shared_subcutaneous.png │ ├── glasso_shared_thyroid.png │ ├── glasso_tft_artery.png │ ├── glasso_tft_lung.png │ ├── glasso_tft_muscle.png │ ├── glasso_tft_nerve.png │ ├── glasso_tft_skin.png │ ├── glasso_tft_subcutaneous.png │ ├── glasso_tft_thyroid.png │ ├── power_wgcna_canonical_artery.png │ ├── power_wgcna_canonical_blood.png │ ├── power_wgcna_canonical_lung.png │ ├── power_wgcna_canonical_muscle.png │ ├── power_wgcna_canonical_nerve.png │ ├── power_wgcna_canonical_skin.png │ ├── power_wgcna_canonical_subcutaneous.png │ ├── power_wgcna_canonical_thyroid.png │ ├── power_wgcna_tft_artery.png │ ├── power_wgcna_tft_blood.png │ ├── power_wgcna_tft_lung.png │ ├── power_wgcna_tft_muscle.png │ ├── power_wgcna_tft_nerve.png │ ├── power_wgcna_tft_skin.png │ ├── power_wgcna_tft_subcutaneous.png │ ├── power_wgcna_tft_thyroid.png │ ├── wgcna-signed_canonical_artery.png │ ├── wgcna-signed_canonical_blood.png │ ├── wgcna-signed_canonical_lung.png │ ├── wgcna-signed_canonical_muscle.png │ ├── wgcna-signed_canonical_nerve.png │ ├── wgcna-signed_canonical_skin.png │ ├── wgcna-signed_canonical_subcutaneous.png │ ├── wgcna-signed_canonical_thyroid.png │ ├── wgcna-signed_shared_artery.png │ ├── wgcna-signed_shared_blood.png │ ├── wgcna-signed_shared_lung.png │ ├── wgcna-signed_shared_muscle.png │ ├── wgcna-signed_shared_nerve.png │ ├── wgcna-signed_shared_skin.png │ ├── wgcna-signed_shared_subcutaneous.png │ ├── wgcna-signed_shared_thyroid.png │ ├── wgcna-signed_tft_artery.png │ ├── wgcna-signed_tft_blood.png │ ├── wgcna-signed_tft_lung.png │ ├── wgcna-signed_tft_muscle.png │ ├── wgcna-signed_tft_nerve.png │ ├── wgcna-signed_tft_skin.png │ ├── wgcna-signed_tft_subcutaneous.png │ ├── wgcna-signed_tft_thyroid.png │ ├── wgcna_canonical_artery.png │ ├── wgcna_canonical_blood.png │ ├── wgcna_canonical_lung.png │ ├── wgcna_canonical_muscle.png │ ├── wgcna_canonical_nerve.png │ ├── wgcna_canonical_skin.png │ ├── wgcna_canonical_subcutaneous.png │ └── wgcna_canonical_thyroid.png └── known_covariates_expression_pve.png ├── publication_figures ├── Rplots.pdf ├── fig1.pdf ├── fig1 │ ├── make_fig1.R │ ├── merged.pdf │ ├── panelc.pdf │ ├── panelf.pdf │ └── paneli.pdf ├── fig2.pdf ├── fig3.pdf ├── fig4.pdf ├── src │ ├── makefig2.R │ ├── makefig3.R │ ├── makefig3old.R │ ├── supp_fig1.R │ ├── supp_fig10.R │ ├── supp_fig11.R │ ├── supp_fig12.R │ ├── supp_fig13.R │ ├── supp_fig14.R │ ├── supp_fig2.R │ ├── supp_fig3.R │ ├── supp_fig4.R │ ├── supp_fig6.R │ ├── supp_fig7.R │ ├── supp_fig8.R │ └── supp_fig9.R ├── suppfig1.pdf ├── suppfig10.pdf ├── suppfig11.pdf ├── suppfig12.pdf ├── suppfig13.pdf ├── suppfig14.pdf ├── suppfig15.pdf ├── suppfig15 │ ├── average_module_size.png │ ├── gray_modules.R │ ├── make_suppfig15.R │ ├── module_size.R │ ├── num_genes_gray_modules.png │ ├── num_modules.R │ ├── num_modules.png │ └── wgcna_module_size.Rds ├── suppfig2.pdf ├── suppfig3.pdf ├── suppfig4.pdf ├── suppfig5.pdf ├── suppfig5 │ ├── Rplots.pdf │ ├── make_suppfig5.R │ ├── pvals.png │ ├── r2.png │ └── suppfig5.pdf ├── suppfig6.pdf ├── suppfig7.pdf ├── suppfig8.pdf └── suppfig9.pdf ├── publication_rmd ├── simulation_example_fig1 │ ├── figure1.Rmd │ ├── figure1.html │ ├── figure1.md │ ├── merged.pdf │ ├── panelc.pdf │ ├── panelf.pdf │ └── paneli.pdf ├── simulation_scale-free_matched_gtex │ ├── alternate_versions │ │ ├── no_scalar │ │ │ ├── generate_sim_data.R │ │ │ ├── infer_nets.R │ │ │ ├── run_sim.sh │ │ │ └── submit_jobs.sh │ │ ├── overlap_confound │ │ │ ├── generate_data.sh │ │ │ ├── generate_sim_data.R │ │ │ ├── infer_nets.R │ │ │ ├── run_sim.sh │ │ │ └── submit_jobs.sh │ │ └── overlap_confound_withsf │ │ │ ├── generate_data.sh │ │ │ ├── generate_sim_data.R │ │ │ ├── infer_nets.R │ │ │ ├── run_sim.sh │ │ │ └── submit_jobs.sh │ ├── weighted_confound │ │ ├── generate_data.sh │ │ ├── generate_sim_data.R │ │ ├── infer_nets.R │ │ ├── markdown │ │ │ ├── simulation_gtex_matched.Rmd │ │ │ └── simulation_gtex_matched.html │ │ ├── run_sim.sh │ │ └── submit_jobs.sh │ └── weighted_confounded_largesample │ │ ├── generate_data.sh │ │ ├── generate_sim_data.R │ │ ├── infer_nets.R │ │ ├── run_sim.sh │ │ ├── slurm-32479419.out │ │ ├── slurm-32481963.out │ │ └── submit_jobs.sh ├── simulation_scale_free │ ├── confounded_data.Rds │ ├── scale_free_sim.Rmd │ ├── scale_free_sim.html │ └── scale_free_sim.nb.html └── tutorial_vignette │ ├── liver_subset_gtex.Rdata │ ├── prepare_liver_gtex_tutorial.R │ ├── tutorial.Rmd │ └── tutorial.html ├── results ├── PR │ ├── pr_density_glasso_canonical_artery.Rds │ ├── pr_density_glasso_canonical_blood.Rds │ ├── pr_density_glasso_canonical_lung.Rds │ ├── pr_density_glasso_canonical_muscle.Rds │ ├── pr_density_glasso_canonical_nerve.Rds │ ├── pr_density_glasso_canonical_skin.Rds │ ├── pr_density_glasso_canonical_subcutaneous.Rds │ ├── pr_density_glasso_canonical_thyroid.Rds │ ├── pr_density_glasso_shared_artery.Rds │ ├── pr_density_glasso_shared_blood.Rds │ ├── pr_density_glasso_shared_lung.Rds │ ├── pr_density_glasso_shared_muscle.Rds │ ├── pr_density_glasso_shared_nerve.Rds │ ├── pr_density_glasso_shared_skin.Rds │ ├── pr_density_glasso_shared_subcutaneous.Rds │ ├── pr_density_glasso_shared_thyroid.Rds │ ├── pr_density_glasso_tft_artery.Rds │ ├── pr_density_glasso_tft_lung.Rds │ ├── pr_density_glasso_tft_muscle.Rds │ ├── pr_density_glasso_tft_nerve.Rds │ ├── pr_density_glasso_tft_skin.Rds │ ├── pr_density_glasso_tft_subcutaneous.Rds │ ├── pr_density_glasso_tft_thyroid.Rds │ ├── pr_density_power_wgcna_canonical_artery.Rds │ ├── pr_density_power_wgcna_canonical_blood.Rds │ ├── pr_density_power_wgcna_canonical_lung.Rds │ ├── pr_density_power_wgcna_canonical_muscle.Rds │ ├── pr_density_power_wgcna_canonical_nerve.Rds │ ├── pr_density_power_wgcna_canonical_skin.Rds │ ├── pr_density_power_wgcna_canonical_subcutaneous.Rds │ ├── pr_density_power_wgcna_canonical_thyroid.Rds │ ├── pr_density_power_wgcna_tft_artery.Rds │ ├── pr_density_power_wgcna_tft_blood.Rds │ ├── pr_density_power_wgcna_tft_lung.Rds │ ├── pr_density_power_wgcna_tft_muscle.Rds │ ├── pr_density_power_wgcna_tft_nerve.Rds │ ├── pr_density_power_wgcna_tft_skin.Rds │ ├── pr_density_power_wgcna_tft_subcutaneous.Rds │ ├── pr_density_power_wgcna_tft_thyroid.Rds │ ├── pr_density_wgcna-signed_canonical_artery.Rds │ ├── pr_density_wgcna-signed_canonical_blood.Rds │ ├── pr_density_wgcna-signed_canonical_lung.Rds │ ├── pr_density_wgcna-signed_canonical_muscle.Rds │ ├── pr_density_wgcna-signed_canonical_nerve.Rds │ ├── pr_density_wgcna-signed_canonical_skin.Rds │ ├── pr_density_wgcna-signed_canonical_subcutaneous.Rds │ ├── pr_density_wgcna-signed_canonical_thyroid.Rds │ ├── pr_density_wgcna-signed_shared_artery.Rds │ ├── pr_density_wgcna-signed_shared_blood.Rds │ ├── pr_density_wgcna-signed_shared_lung.Rds │ ├── pr_density_wgcna-signed_shared_muscle.Rds │ ├── pr_density_wgcna-signed_shared_nerve.Rds │ ├── pr_density_wgcna-signed_shared_skin.Rds │ ├── pr_density_wgcna-signed_shared_subcutaneous.Rds │ ├── pr_density_wgcna-signed_shared_thyroid.Rds │ ├── pr_density_wgcna-signed_tft_artery.Rds │ ├── pr_density_wgcna-signed_tft_blood.Rds │ ├── pr_density_wgcna-signed_tft_lung.Rds │ ├── pr_density_wgcna-signed_tft_muscle.Rds │ ├── pr_density_wgcna-signed_tft_nerve.Rds │ ├── pr_density_wgcna-signed_tft_skin.Rds │ ├── pr_density_wgcna-signed_tft_subcutaneous.Rds │ ├── pr_density_wgcna-signed_tft_thyroid.Rds │ ├── pr_density_wgcna_canonical_artery.Rds │ ├── pr_density_wgcna_canonical_blood.Rds │ ├── pr_density_wgcna_canonical_lung.Rds │ ├── pr_density_wgcna_canonical_muscle.Rds │ ├── pr_density_wgcna_canonical_nerve.Rds │ ├── pr_density_wgcna_canonical_skin.Rds │ ├── pr_density_wgcna_canonical_subcutaneous.Rds │ └── pr_density_wgcna_canonical_thyroid.Rds ├── tissue_pve.Rds └── wgcna_module_size.Rds ├── rmd_analysis └── total_expression_pve_allcovariates.Rmd ├── shellscripts ├── corrnet.sh ├── data_correction.sh ├── dirconfig ├── get_true_positive.sh ├── glasso_template.sh ├── pr_corrnet.sh ├── pr_glasso.sh ├── pr_power_wgcna.sh ├── pr_shared.sh ├── pr_signed_wgcna.sh ├── pr_wgcna.sh ├── run_pipeline.sh ├── signed_wgcna.sh ├── submit_jobs_glasso.sh ├── submit_jobs_wgcna_power_vary.sh ├── template_power_vary_wgcna.sh └── wgcna.sh └── src ├── attach_gc_recount.R ├── check_cross_mapping_thyroid_top500.R ├── compute_cross_mapping_pathway_proportion.R ├── compute_gc_estimates.R ├── compute_gene_GC.py ├── compute_pr.R ├── config.R ├── covariate_correction.R ├── dataDownload.R ├── functions.R ├── get_overlapping_geneid_genesymbol.R ├── get_shared_pathway_edges.R ├── infer_corrnet.R ├── infer_glasso.R ├── infer_wgcna.R ├── infer_wgcna_vary_power.R ├── known_covariates_expression_pve.R ├── multiple_covariate_correction.R ├── pc_correction.R ├── pr_corrnet.R ├── pr_glasso.R ├── pr_signed_wgcna.R ├── pr_wgcna.R ├── process_gtex.R ├── select_genes.R ├── select_genes_pertiss.R ├── single_covariate_correction.R ├── variance_analysis.R ├── wgcna_comparison.R └── wgcna_module_enrichment.R /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/leekgroup/networks_correction/HEAD/.gitignore -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/leekgroup/networks_correction/HEAD/README.md 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