├── .Rprofile ├── .gitignore ├── Makefile ├── R ├── README.md ├── nullalthist.R ├── plot_FDReg_hist.R └── set_plot_colors.R ├── README.md ├── analysis ├── CompareEEvsETmodel.Rmd ├── CompareEEvsETmodel.html ├── IPvsEM.Rmd ├── IPvsEM.html ├── Makefile ├── adaptive_shrinkage.Rmd ├── adaptive_shrinkage.html ├── ash_npmle.Rmd ├── ash_npmle.html ├── checkIP.Rmd ├── checkIP.html ├── check_mixfdr_lownoise.Rmd ├── check_mixfdr_lownoise.html ├── chunk-options.R ├── efron.fcr.Rmd ├── efron.fcr.html ├── estimate_mode.Rmd ├── estimate_mode.html ├── figure │ ├── IPvsEM.Rmd │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ └── unnamed-chunk-4-1.png │ ├── adaptive_shrinkage.Rmd │ │ ├── plotting lfsr-1.png │ │ ├── plotting-1.png │ │ ├── run-ash-ET-1.png │ │ ├── run-ash-ET-2.png │ │ ├── sehist-1.png │ │ ├── unnamed-chunk-1-1.png │ │ └── volcano-1.png │ ├── ash_npmle.Rmd │ │ ├── unnamed-chunk-1-1.png │ │ ├── unnamed-chunk-1-2.png │ │ └── unnamed-chunk-2-1.png │ ├── checkIP.Rmd │ │ ├── unnamed-chunk-1-1.png │ │ └── unnamed-chunk-2-1.png │ ├── check_mixfdr_lownoise.Rmd │ │ ├── unnamed-chunk-1-1.png │ │ └── unnamed-chunk-2-1.png │ ├── efron.fcr.Rmd │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-3-2.png │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-4-2.png │ │ ├── unnamed-chunk-4-3.png │ │ ├── unnamed-chunk-5-1.png │ │ ├── unnamed-chunk-5-2.png │ │ ├── unnamed-chunk-5-3.png │ │ ├── unnamed-chunk-6-1.png │ │ ├── unnamed-chunk-7-1.png │ │ └── unnamed-chunk-8-1.png │ ├── investigate_hu_badcoverage.Rmd │ │ ├── unnamed-chunk-4-1.png │ │ ├── unnamed-chunk-4-2.png │ │ ├── unnamed-chunk-6-1.png │ │ └── unnamed-chunk-6-2.png │ ├── make_GOODPOOR_figs.Rmd │ │ ├── GOODPOOReg_hist-1.pdf │ │ ├── GOODPOOReg_scatter-1.pdf │ │ ├── lfsr_vs_pval_GOODPOOR-1.pdf │ │ ├── lfsr_vs_pval_GOODPOOR-2.pdf │ │ ├── lfsr_vs_pval_GOODPOOR_single-1.pdf │ │ ├── lfsr_vs_pval_GOODPOOR_single-2.pdf │ │ ├── lfsr_vs_pval_GOODPOOR_single-3.pdf │ │ ├── lfsr_vs_pval_GOODPOOR_single-4.pdf │ │ ├── roc-curve-1.pdf │ │ ├── tp_vs_fp-1.pdf │ │ └── unnamed-chunk-3-1.png │ ├── makefig_FDReg.Rmd │ │ ├── decomp_ZA-1.pdf │ │ ├── decomp_ZA_poster-1.pdf │ │ ├── unnamed-chunk-1-1.png │ │ └── unnamed-chunk-2-1.png │ ├── plot_cdf_eg.Rmd │ │ ├── egcdf-1.pdf │ │ ├── egcdf-reduce-1.pdf │ │ ├── egcdf-reduce-with-npmle-1.pdf │ │ ├── egcdf-reduce-with-npmle-2.pdf │ │ ├── mean_cdf-1.pdf │ │ ├── mean_cdf-reduce-1.pdf │ │ ├── mean_cdf_nopen-1.pdf │ │ └── mean_cdf_nopen-reduce-1.pdf │ ├── plot_egdens.Rmd │ │ └── scenario_density-1.pdf │ ├── plot_lfsr.Rmd │ │ ├── plot_lfdr-1.pdf │ │ ├── plot_lfdr-1.png │ │ ├── plot_lfsr-1.pdf │ │ ├── plot_lfsr-1.png │ │ ├── plot_lfsr_s-1.pdf │ │ ├── plot_lfsr_s-1.png │ │ ├── plot_lfsr_s_nn-1.pdf │ │ └── plot_lfsr_s_nn-1.png │ ├── plot_pi0est.Rmd │ │ └── plot_pi0est-1.pdf │ ├── referee.response.Rmd │ │ ├── unnamed-chunk-1-1.png │ │ └── unnamed-chunk-1-2.png │ ├── referee_uaza.Rmd │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-3-1.png │ │ ├── unnamed-chunk-4-1.png │ │ └── unnamed-chunk-5-1.png │ └── summarize_dsc_znull.Rmd │ │ ├── unnamed-chunk-2-1.png │ │ ├── unnamed-chunk-2-2.png │ │ └── unnamed-chunk-2-3.png ├── index.Rmd ├── index.html ├── investigate_hu_badcoverage.Rmd ├── investigate_hu_badcoverage.html ├── make_GOODPOOR_figs.Rmd ├── make_GOODPOOR_figs.html ├── makefig_FDReg.Rmd ├── makefig_FDReg.html ├── metaplot_examples.Rmd ├── metaplot_examples.html ├── plot_cdf_eg.Rmd ├── plot_cdf_eg.html ├── plot_egdens.Rmd ├── plot_egdens.html ├── plot_egdens2.Rmd ├── plot_egdens2.html ├── plot_lfsr.Rmd ├── plot_lfsr.html ├── plot_pi0est.Rmd ├── plot_pi0est.html ├── referee.response.Rmd ├── referee.response.html ├── referee_uaza.Rmd ├── referee_uaza.html ├── summarize_coverage.Rmd ├── summarize_coverage.html ├── summarize_dsc_znull.Rmd ├── summarize_dsc_znull.html ├── table │ ├── README.md │ ├── coverage_all.tex │ ├── coverage_all_nopen.tex │ ├── coverage_neg.tex │ ├── coverage_neg_nopen.tex │ ├── coverage_pos.tex │ ├── coverage_pos_nopen.tex │ ├── scoverage_all.tex │ ├── scoverage_all_nopen.tex │ ├── scoverage_neg.tex │ ├── scoverage_neg_nopen.tex │ ├── scoverage_pos.tex │ └── scoverage_pos_nopen.tex ├── template.Rmd └── template.html ├── ash-packrat.Rproj ├── code ├── Makefile ├── README.md ├── dsc-opt │ ├── methods │ │ └── ash.multiopt.wrapper.R │ └── run_dsc_opt.R └── dsc-shrink │ ├── add_methods.R │ ├── add_methods.null.R │ ├── add_named_scenarios.R │ ├── add_scenarios.null.R │ ├── datamakers │ ├── datamaker.R │ ├── null_t_datamaker.R │ └── null_z_datamaker.R │ ├── methods │ ├── ash.wrapper.R │ ├── locfdr.wrapper.R │ ├── mixfdr.wrapper.R │ └── qvalue.wrapper.R │ ├── run_dsc.R │ ├── run_dsc_mini.R │ ├── run_dsc_znull.R │ └── score.R ├── data └── README.md ├── output └── README.md ├── packrat ├── init.R ├── packrat.lock ├── packrat.opts └── src │ ├── mixfdr │ └── mixfdr_1.0.tar.gz │ └── packrat │ └── packrat_0.4.4.tar.gz ├── paper ├── Makefile ├── README.md ├── main.bbl ├── 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