├── .Rbuildignore ├── .gitignore ├── .travis.yml ├── DESCRIPTION ├── LICENSE ├── LICENSE.md ├── NAMESPACE ├── R ├── RcppExports.R ├── compute_covs.R ├── cov_udi.R ├── data2cov.R ├── ed.R ├── est_cor.R ├── extreme_deconvolution.R ├── get_functions.R ├── likelihoods_origdata.R ├── likelihoods_scaleddata.R ├── mash.R ├── matrix_utils.R ├── opt.R ├── plots.R ├── posterior.R ├── posterior_common_cov.R ├── posterior_lowmem.R ├── set_data.R ├── simulations.R ├── simulations_contrast.R └── todo.R ├── README.md ├── _pkgdown.yaml ├── cleanup ├── configure ├── configure.win ├── docs ├── 404.html ├── LICENSE-text.html ├── LICENSE.html ├── articles │ ├── MASH_baseline.pdf │ ├── eQTL_outline.html │ ├── eQTL_outline_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── header-attrs-2.9 │ │ │ └── header-attrs.js │ ├── flash_mash.html │ ├── flash_mash_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── header-attrs-2.9 │ │ │ └── header-attrs.js │ ├── index.html │ ├── intro_correlations.html │ ├── intro_correlations_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── header-attrs-2.9 │ │ │ └── header-attrs.js │ ├── intro_mash.html │ ├── intro_mash_dd.html │ ├── intro_mash_dd_files │ │ └── header-attrs-2.9 │ │ │ └── header-attrs.js │ ├── intro_mash_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ ├── figure-html │ │ │ ├── unnamed-chunk-11-1.png │ │ │ └── unnamed-chunk-12-1.png │ │ └── header-attrs-2.9 │ │ │ └── header-attrs.js │ ├── intro_mashbaselinemean.html │ ├── intro_mashbaselinemean_files │ │ └── header-attrs-2.9 │ │ │ └── header-attrs.js │ ├── intro_mashcommonbaseline.html │ ├── intro_mashcommonbaseline_files │ │ ├── accessible-code-block-0.0.1 │ │ │ └── empty-anchor.js │ │ └── header-attrs-2.9 │ │ │ └── header-attrs.js │ ├── intro_mashnobaseline.html │ ├── mash_sampling.html │ ├── mash_sampling_files │ │ ├── figure-html │ │ │ ├── unnamed-chunk-5-1.png │ │ │ ├── unnamed-chunk-6-1.png │ │ │ └── unnamed-chunk-7-1.png │ │ └── header-attrs-2.9 │ │ │ └── header-attrs.js │ ├── simulate_noncanon.html │ └── simulate_noncanon_files │ │ └── header-attrs-2.9 │ │ └── header-attrs.js ├── authors.html ├── bootstrap-toc.css ├── bootstrap-toc.js ├── docsearch.css ├── docsearch.js ├── index.html ├── link.svg ├── pkgdown.css ├── pkgdown.js ├── pkgdown.yml ├── reference │ ├── ExDeconDemo_c.log │ ├── ExDeconDemo_loglike.log │ ├── Rplot001.png │ ├── bovy_wrapper.html │ ├── calc_lik_matrix.html │ ├── calc_lik_matrix_common_cov.html │ ├── calc_lik_vector.html │ ├── calc_relative_lik_matrix.html │ ├── compute_alt_loglik_from_matrix_and_pi.html │ ├── compute_loglik_from_matrix_and_pi.html │ ├── compute_null_loglik_from_matrix.html │ ├── compute_posterior_matrices.html │ ├── compute_posterior_matrices_common_cov_R.html │ ├── compute_posterior_matrices_general_R.html │ ├── compute_posterior_weights.html │ ├── compute_vloglik_from_matrix_and_pi.html │ ├── contrast_matrix.html │ ├── cov_all_zeros.html │ ├── cov_canonical.html │ ├── cov_ed.html │ ├── cov_equal_effects.html │ ├── cov_first_singleton.html │ ├── cov_flash.html │ ├── cov_from_factors.html │ ├── cov_pca.html │ ├── cov_simple_het.html │ ├── cov_udi.html │ ├── cov_udi_single.html │ ├── estimate_null_correlation.html │ ├── estimate_null_correlation_simple.html │ ├── expand_cov.html │ ├── extreme_deconvolution.html │ ├── get_estimated_pi.html │ ├── get_log10bf.html │ ├── get_n_significant_conditions.html │ ├── get_pairwise_sharing.html │ ├── get_pairwise_sharing_from_samples.html │ ├── get_posterior_condition_wise_summary.html │ ├── get_samples.html │ ├── get_significant_results.html │ ├── index.html │ ├── initialize_pi.html │ ├── is_common_cov_Shat.html │ ├── is_common_cov_Shat_alpha.html │ ├── make_names.html │ ├── mash-1.png │ ├── mash.html │ ├── mash_1by1.html │ ├── mash_compute_loglik.html │ ├── mash_compute_posterior_matrices.html │ ├── mash_compute_vloglik.html │ ├── mash_estimate_corr_em.html │ ├── mash_plot_meta-1.png │ ├── mash_plot_meta.html │ ├── mash_set_data.html │ ├── mash_set_data_contrast.html │ ├── mash_update_data.html │ ├── nonneg.html │ ├── optimize_pi.html │ ├── posterior_cov.html │ ├── posterior_mean.html │ ├── posterior_mean_matrix.html │ ├── scale_cov.html │ ├── sim_contrast1.html │ ├── sim_contrast2.html │ ├── simple_sims.html │ ├── simple_sims2.html │ ├── teem_wrapper.html │ └── udi_model_matrix.html └── sitemap.xml ├── inst ├── CITATION ├── COPYRIGHTS ├── code │ ├── compare_ed_vs_teem.Rmd │ ├── get_est_null_cor.R │ ├── test1.R │ ├── test_lik.R │ └── test_post.R └── misc │ ├── LICENSE-extreme-deconvolution │ ├── post-commit.sh │ ├── pre-commit.sh │ └── uncrustify_default.cfg ├── man ├── bovy_wrapper.Rd ├── calc_lik_matrix.Rd ├── calc_lik_matrix_common_cov.Rd ├── calc_lik_vector.Rd ├── calc_relative_lik_matrix.Rd ├── compute_alt_loglik_from_matrix_and_pi.Rd ├── compute_loglik_from_matrix_and_pi.Rd ├── compute_null_loglik_from_matrix.Rd ├── compute_posterior_matrices.Rd ├── compute_posterior_matrices_common_cov_R.Rd ├── compute_posterior_matrices_general_R.Rd ├── compute_posterior_weights.Rd ├── compute_vloglik_from_matrix_and_pi.Rd ├── contrast_matrix.Rd ├── cov_all_zeros.Rd ├── cov_canonical.Rd ├── cov_ed.Rd ├── cov_equal_effects.Rd ├── cov_first_singleton.Rd ├── cov_flash.Rd ├── cov_from_factors.Rd ├── cov_pca.Rd ├── cov_simple_het.Rd ├── cov_udi.Rd ├── cov_udi_single.Rd ├── estimate_null_correlation_simple.Rd ├── expand_cov.Rd ├── extreme_deconvolution.Rd ├── get_estimated_pi.Rd ├── get_log10bf.Rd ├── get_n_significant_conditions.Rd ├── get_pairwise_sharing.Rd ├── get_pairwise_sharing_from_samples.Rd ├── get_posterior_condition_wise_summary.Rd ├── get_samples.Rd ├── get_significant_results.Rd ├── make_names.Rd ├── mash.Rd ├── mash_1by1.Rd ├── mash_compute_loglik.Rd ├── mash_compute_posterior_matrices.Rd ├── mash_compute_vloglik.Rd ├── mash_estimate_corr_em.Rd ├── mash_plot_meta.Rd ├── mash_set_data.Rd ├── mash_set_data_contrast.Rd ├── mash_update_data.Rd ├── optimize_pi.Rd ├── posterior_cov.Rd ├── posterior_mean.Rd ├── posterior_mean_matrix.Rd ├── scale_cov.Rd ├── sim_contrast1.Rd ├── sim_contrast2.Rd ├── simple_sims.Rd ├── simple_sims2.Rd ├── teem_wrapper.Rd └── udi_model_matrix.Rd ├── mashr.Rproj ├── src ├── Makevars.in ├── RcppExports.cpp ├── extreme_deconvolution.cpp ├── mash.cpp └── mash.h ├── tests ├── testthat.R └── testthat │ ├── calc_lik_matrix_data.RData │ ├── compute_posterior_matrices_data.RData │ ├── estimate_null_cor.rds │ ├── estimate_null_cor_alpha.rds │ ├── test_Varray.R │ ├── test_ash.R │ ├── test_cov.R │ ├── test_cov_udi.R │ ├── test_cpp_computation.R │ ├── test_ed.R │ ├── test_estimate_cor.R │ ├── test_getfunctions.R │ ├── test_likelihood.R │ ├── test_likelihood_common_cov.R │ ├── test_posterior.R │ ├── test_posterior_common_cov.R │ ├── test_precomputed.R │ ├── test_sampling.R │ ├── test_set_data.R │ └── test_simple_sims.R 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