├── .Rbuildignore ├── .github ├── dependabot.yml ├── environment │ └── pixi.toml ├── rattler-build_container.df ├── recipe │ ├── recipe.yaml │ ├── variant_r43.yaml │ └── variant_r44.yaml └── workflows │ ├── README.md │ ├── ci.yml │ ├── conda_build.yml │ ├── create_toml_from_yaml.sh │ ├── dependabot_automerge.yml │ ├── merge.yml │ ├── release.yml │ └── update-documentation.yml ├── .gitignore ├── DESCRIPTION ├── LICENSE ├── NAMESPACE ├── R ├── LD.R ├── RcppExports.R ├── allele_qc.R ├── colocboost_pipeline.R ├── compute_qtl_enrichment.R ├── ctwas_wrapper.R ├── dentist_qc.R ├── encoloc.R ├── file_utils.R ├── fsusie_wrapper.R ├── mash_wrapper.R ├── misc.R ├── mr.R ├── mrmash_wrapper.R ├── multigene_udr.R ├── multitrait_data.R ├── multivariate_pipeline.R ├── plot.R ├── quail_rank_score.R ├── quail_vqtl.R ├── quantile_twas.R ├── quantile_twas_weight.R ├── raiss.R ├── regularized_regression.R ├── slalom.R ├── sumstats_qc.R ├── susie_wrapper.R ├── twas.R ├── twas_weights.R ├── univariate_pipeline.R └── univariate_rss_diagnostics.R ├── README.md ├── cleanup ├── configure ├── data └── multitrait_data.RData ├── inst ├── code │ ├── fastenloc_archive │ │ ├── README.md │ │ ├── controller.cc │ │ ├── controller.h │ │ ├── main.cc │ │ ├── sigCluster.cc │ │ └── sigCluster.h │ └── tensorqtl_postprocessor.R ├── misc │ ├── format_r_code.sh │ ├── post-commit.sh │ ├── pre-commit.sh │ └── uncrustify_default.cfg └── prototype │ ├── Dentist_R_cpp_comparison.ipynb │ ├── RAISS_R_python_comparison.ipynb │ ├── SDPR_testing │ ├── SDPR_chr22.txt │ ├── SDPR_testing.ipynb │ ├── chr10_region_posterior.csv │ ├── marginal_rss.txt │ └── output_matrix_1.txt │ ├── enrich_coloc_example.ipynb │ ├── generate_test_for_prs_cs.R │ ├── raiss_prototype.ipynb │ ├── run_prs_cs_test.py │ └── slalom_R_python_comparison.ipynb ├── man ├── QUAIL_pipeline.Rd ├── QUAIL_rank_score_pipeline.Rd ├── adjust_susie_weights.Rd ├── align_variant_names.Rd ├── allele_qc.Rd ├── auto_decision.Rd ├── batch_load_twas_weights.Rd ├── bayes_a_rss_weights.Rd ├── bayes_a_weights.Rd ├── bayes_alphabet_rss_weights.Rd ├── bayes_alphabet_weights.Rd ├── bayes_c_rss_weights.Rd ├── bayes_c_weights.Rd ├── bayes_l_rss_weights.Rd ├── bayes_l_weights.Rd ├── bayes_n_rss_weights.Rd ├── bayes_n_weights.Rd ├── bayes_r_rss_weights.Rd ├── bayes_r_weights.Rd ├── coloc_post_processor.Rd ├── coloc_wrapper.Rd ├── colocboost_analysis_pipeline.Rd ├── compute_qtl_enrichment.Rd ├── corr_filter.Rd ├── ctwas_ld_loader.Rd ├── dentist.Rd ├── dentist_single_window.Rd ├── extract_LD_for_region.Rd ├── extract_cs_info.Rd ├── extract_flatten_sumstats_from_nested.Rd ├── extract_top_pip_info.Rd ├── filter_X_with_Y.Rd ├── filter_molecular_events.Rd ├── filter_variants_by_ld_reference.Rd ├── find_data.Rd ├── find_duplicate_variants.Rd ├── find_valid_file_path.Rd ├── fsusie_get_cs.Rd ├── fsusie_wrapper.Rd ├── gbayes_rss.Rd ├── get_cormat.Rd ├── get_ctwas_meta_data.Rd ├── get_susie_result.Rd ├── harmonize_twas.Rd ├── lbf_to_alpha.Rd ├── load_LD_matrix.Rd ├── load_genotype_region.Rd ├── load_multicontext_sumstats.Rd ├── load_multitask_regional_data.Rd ├── load_quantile_twas_weights.Rd ├── load_regional_association_data.Rd ├── load_regional_functional_data.Rd ├── load_regional_multivariate_data.Rd ├── load_regional_regression_data.Rd ├── load_regional_univariate_data.Rd ├── load_rss_data.Rd ├── load_tsv_region.Rd ├── load_twas_weights.Rd ├── manhattan_plot.Rd ├── merge_sumstats_matrices.Rd ├── mr_analysis.Rd ├── mr_ash_rss.Rd ├── mr_ash_rss_weights.Rd ├── mr_format.Rd ├── mrash_weights.Rd ├── mrmash_wrapper.Rd ├── multicontext_ld_clumping.Rd ├── multigene_udr.Rd ├── multivariate_analysis_pipeline.Rd ├── parse_cs_corr.Rd ├── perform_qr_analysis.Rd ├── prs_cs.Rd ├── prs_cs_weights.Rd ├── qr_screen.Rd ├── quantile_twas_weight_pipeline.Rd ├── raiss.Rd ├── region_to_df.Rd ├── rescale_cov_w0.Rd ├── rss_analysis_pipeline.Rd ├── rss_basic_qc.Rd ├── sdpr.Rd ├── sdpr_weights.Rd ├── slalom.Rd ├── summary_stats_qc.Rd ├── susie_post_processor.Rd ├── susie_rss_pipeline.Rd ├── susie_rss_qc.Rd ├── susie_rss_wrapper.Rd ├── trim_ctwas_variants.Rd ├── twas_analysis.Rd ├── twas_joint_z.Rd ├── twas_multivariate_weights_pipeline.Rd ├── twas_pipeline.Rd ├── twas_predict.Rd ├── twas_weights.Rd ├── twas_weights_cv.Rd ├── twas_weights_pipeline.Rd ├── twas_z.Rd ├── univariate_analysis_pipeline.Rd ├── venn.Rd ├── xqtl_enrichment_wrapper.Rd └── z_to_pvalue.Rd ├── src ├── Makevars.in ├── RcppExports.cpp ├── dentist_iterative_impute.cpp ├── function_pool.cpp ├── function_pool.h ├── mr_ash.cpp ├── mr_ash.h ├── prscs_mcmc.cpp ├── prscs_mcmc.h ├── qtl_enrichment.cpp ├── qtl_enrichment.hpp ├── sdpr.cpp ├── sdpr_mcmc.cpp ├── sdpr_mcmc.h ├── simde │ ├── arm │ │ ├── neon.h │ │ └── sve.h │ └── x86 │ │ ├── aes.h │ │ ├── avx.h │ │ ├── avx2.h │ │ ├── avx512.h │ │ ├── clmul.h │ │ ├── f16c.h │ │ ├── fma.h │ │ ├── gfni.h │ │ ├── mmx.h │ │ ├── sse.h │ │ ├── sse2.h │ │ ├── sse3.h │ │ ├── sse4.1.h │ │ ├── sse4.2.h │ │ ├── ssse3.h │ │ ├── svml.h │ │ └── xop.h └── sse_mathfun.h ├── tests ├── testthat.R └── testthat │ ├── test_LD.R │ ├── test_allele_qc.R │ ├── test_compute_qtl_enrichment.R │ ├── test_data │ ├── LD_block_1.chr1_1000_1200.float16.bim │ ├── LD_block_1.chr1_1000_1200.float16.txt.xz │ ├── LD_block_2.chr1_1200_1400.float16.bim │ ├── LD_block_2.chr1_1200_1400.float16.txt.xz │ ├── LD_block_3.chr1_1400_1600.float16.bim │ ├── LD_block_3.chr1_1400_1600.float16.txt.xz │ ├── LD_block_4.chr1_1600_1800.float16.bim │ ├── LD_block_4.chr1_1600_1800.float16.txt.xz │ ├── LD_block_5.chr1_1800_2000.float16.bim │ ├── LD_block_5.chr1_1800_2000.float16.txt.xz │ ├── dummy_data.pgen │ ├── dummy_data.psam │ ├── dummy_data.pvar │ ├── protocol_example.genotype.bed │ ├── protocol_example.genotype.bim │ └── protocol_example.genotype.fam │ ├── test_dentist_qc.R │ ├── test_encoloc.R │ ├── test_file_utils.R │ ├── test_mash_wrapper.R │ ├── test_misc.R │ ├── test_mr.R │ ├── test_mrmash_wrapper.R │ ├── test_raiss.R │ 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