LICENSE
README.md
pyproject.toml
src/gwaslab/__init__.py
src/gwaslab/__main__.py
src/gwaslab/cache_manager.py
src/gwaslab/g_Sumstats.py
src/gwaslab/g_SumstatsMulti.py
src/gwaslab/g_SumstatsPair.py
src/gwaslab/g_SumstatsSet.py
src/gwaslab/g_SumstatsT.py
src/gwaslab/g_Sumstats_polars.py
src/gwaslab.egg-info/PKG-INFO
src/gwaslab.egg-info/SOURCES.txt
src/gwaslab.egg-info/dependency_links.txt
src/gwaslab.egg-info/entry_points.txt
src/gwaslab.egg-info/requires.txt
src/gwaslab.egg-info/top_level.txt
src/gwaslab/CLI/cli.py
src/gwaslab/bd/bd_build.py
src/gwaslab/bd/bd_chromosome_mapper.py
src/gwaslab/bd/bd_common_data.py
src/gwaslab/bd/bd_config.py
src/gwaslab/bd/bd_download.py
src/gwaslab/bd/bd_get_hapmap3.py
src/gwaslab/bd/bd_sex_chromosomes.py
src/gwaslab/bd/bd_sumstats_formats.py
src/gwaslab/data/config.json
src/gwaslab/data/formatbook.json
src/gwaslab/data/reference.json
src/gwaslab/data/chains/hg19ToHg38.over.chain.gz
src/gwaslab/data/chains/hg38ToHg19.over.chain.gz
src/gwaslab/data/chromosomes/chromosomes_nc.json
src/gwaslab/data/chrx_par/chrx_par_hg19.bed.gz
src/gwaslab/data/chrx_par/chrx_par_hg38.bed.gz
src/gwaslab/data/cytoband/cytoBand_hg19.txt.gz
src/gwaslab/data/cytoband/cytoBand_hg38.txt.gz
src/gwaslab/data/hapmap3_SNPs/hapmap3_db150_hg19.snplist.gz
src/gwaslab/data/hapmap3_SNPs/hapmap3_db151_hg38.snplist.gz
src/gwaslab/data/high_ld/high_ld_hla_hg19.bed.gz
src/gwaslab/data/high_ld/high_ld_hla_hg38.bed.gz
src/gwaslab/downstream/__init__.py
src/gwaslab/downstream/ds_result_manager.py
src/gwaslab/extension/__init__.py
src/gwaslab/extension/extension_version.py
src/gwaslab/extension/gwas_sumstats_tools/validate_ssf.py
src/gwaslab/extension/gwascatalog/__init__.py
src/gwaslab/extension/gwascatalog/gwascatalog.py
src/gwaslab/extension/ldsc/ldsc_irwls.py
src/gwaslab/extension/ldsc/ldsc_jackknife.py
src/gwaslab/extension/ldsc/ldsc_ldscore.py
src/gwaslab/extension/ldsc/ldsc_parse.py
src/gwaslab/extension/ldsc/ldsc_regressions.py
src/gwaslab/extension/ldsc/ldsc_sumstats.py
src/gwaslab/extension/mrmega/__init__.py
src/gwaslab/extension/mrmega/mrmega.py
src/gwaslab/extension/multisusie/__init__.py
src/gwaslab/extension/multisusie/susiepy.py
src/gwaslab/extension/multisusie/susiepy_ss.py
src/gwaslab/extension/prscs/precs_mcmc_gtb2.py
src/gwaslab/extension/prscs/prscs_gigrnd.py
src/gwaslab/extension/prscs/prscs_gigrnd2.py
src/gwaslab/extension/prscs/prscs_mcmc_gtb.py
src/gwaslab/extension/prscs/prscs_parse_genet.py
src/gwaslab/hm/hm_assign_rsid.py
src/gwaslab/hm/hm_casting.py
src/gwaslab/hm/hm_casting_polars.py
src/gwaslab/hm/hm_check_af.py
src/gwaslab/hm/hm_harmonize_sumstats.py
src/gwaslab/hm/hm_infer_with_af.py
src/gwaslab/hm/hm_liftover_v2.py
src/gwaslab/info/g_Log.py
src/gwaslab/info/g_Sumstats_summary.py
src/gwaslab/info/g_meta.py
src/gwaslab/info/g_object_helper.py
src/gwaslab/info/g_vchange_status.py
src/gwaslab/info/g_vchange_status_polars.py
src/gwaslab/info/g_version.py
src/gwaslab/io/__init__.py
src/gwaslab/io/io_bedpe.py
src/gwaslab/io/io_bigwig_bigbed.py
src/gwaslab/io/io_chain.py
src/gwaslab/io/io_fasta.py
src/gwaslab/io/io_gtf.py
src/gwaslab/io/io_gwaslab_standard.py
src/gwaslab/io/io_input_type.py
src/gwaslab/io/io_load_ld.py
src/gwaslab/io/io_plink.py
src/gwaslab/io/io_preformat_input.py
src/gwaslab/io/io_preformat_input_polars.py
src/gwaslab/io/io_process_kwargs.py
src/gwaslab/io/io_read_ldsc.py
src/gwaslab/io/io_read_pipcs.py
src/gwaslab/io/io_read_tabular.py
src/gwaslab/io/io_to_formats.py
src/gwaslab/io/io_to_pickle.py
src/gwaslab/io/io_ucsc_bed.py
src/gwaslab/io/io_vcf.py
src/gwaslab/qc/qc_build.py
src/gwaslab/qc/qc_check_datatype.py
src/gwaslab/qc/qc_check_datatype_polars.py
src/gwaslab/qc/qc_decorator.py
src/gwaslab/qc/qc_fix_sumstats.py
src/gwaslab/qc/qc_fix_sumstats_polars.py
src/gwaslab/qc/qc_normalize_args.py
src/gwaslab/qc/qc_pattern.py
src/gwaslab/qc/qc_researved_header.json
src/gwaslab/qc/qc_reserved_headers.py
src/gwaslab/qc/qc_sanity_check.py
src/gwaslab/util/util_abf_finemapping.py
src/gwaslab/util/util_ex_calculate_ldmatrix.py
src/gwaslab/util/util_ex_calculate_prs.py
src/gwaslab/util/util_ex_gwascatalog.py
src/gwaslab/util/util_ex_infer_ancestry.py
src/gwaslab/util/util_ex_ldproxyfinder.py
src/gwaslab/util/util_ex_ldsc.py
src/gwaslab/util/util_ex_match_ldmatrix.py
src/gwaslab/util/util_ex_phewwas.py
src/gwaslab/util/util_ex_plink_filter.py
src/gwaslab/util/util_ex_process_h5.py
src/gwaslab/util/util_ex_process_ref.py
src/gwaslab/util/util_ex_run_clumping.py
src/gwaslab/util/util_ex_run_magma.py
src/gwaslab/util/util_ex_run_mtag.py
src/gwaslab/util/util_ex_run_multisusie.py
src/gwaslab/util/util_ex_run_prscs.py
src/gwaslab/util/util_ex_run_scdrs.py
src/gwaslab/util/util_in_calculate_gc.py
src/gwaslab/util/util_in_calculate_power.py
src/gwaslab/util/util_in_convert_h2.py
src/gwaslab/util/util_in_correct_winnerscurse.py
src/gwaslab/util/util_in_estimate_ess.py
src/gwaslab/util/util_in_fill_data.py
src/gwaslab/util/util_in_filter_value.py
src/gwaslab/util/util_in_get_density.py
src/gwaslab/util/util_in_get_sig.py
src/gwaslab/util/util_in_merge.py
src/gwaslab/util/util_in_meta.py
src/gwaslab/util/util_in_meta_polars.py
src/gwaslab/util/util_in_simulate.py
src/gwaslab/util/util_in_snphwe.py
src/gwaslab/util/cwrapper/__init__.py
src/gwaslab/util/cwrapper/util_ex_command_runner.py
src/gwaslab/util/general/__init__.py
src/gwaslab/util/general/util_ex_result_manager.py
src/gwaslab/util/general/util_path_manager.py
src/gwaslab/util/general/util_wrapper_log.py
src/gwaslab/util/pwrapper/__init__.py
src/gwaslab/util/pwrapper/util_ex_python_runner.py
src/gwaslab/util/rwrapper/util_ex_r_runner.py
src/gwaslab/util/rwrapper/util_ex_run_2samplemr.py
src/gwaslab/util/rwrapper/util_ex_run_ccgwas.py
src/gwaslab/util/rwrapper/util_ex_run_coloc.py
src/gwaslab/util/rwrapper/util_ex_run_hyprcoloc.py
src/gwaslab/util/rwrapper/util_ex_run_mesusie.py
src/gwaslab/util/rwrapper/util_ex_run_mesusie2.py
src/gwaslab/util/rwrapper/util_ex_run_susie.py
src/gwaslab/util/rwrapper/util_ex_run_susie2.py
src/gwaslab/view/view_report.py
src/gwaslab/view/view_sumstats.py
src/gwaslab/viz/viz_aux_annotate_plot.py
src/gwaslab/viz/viz_aux_chromatin.py
src/gwaslab/viz/viz_aux_panel.py
src/gwaslab/viz/viz_aux_params.py
src/gwaslab/viz/viz_aux_params.txt
src/gwaslab/viz/viz_aux_params_registry.txt
src/gwaslab/viz/viz_aux_property.py
src/gwaslab/viz/viz_aux_quickfix.py
src/gwaslab/viz/viz_aux_reposition_text.py
src/gwaslab/viz/viz_aux_save_figure.py
src/gwaslab/viz/viz_aux_style_options.py
src/gwaslab/viz/viz_aux_xaxis_manager.py
src/gwaslab/viz/viz_plot_arc.py
src/gwaslab/viz/viz_plot_associations.py
src/gwaslab/viz/viz_plot_compare_af.py
src/gwaslab/viz/viz_plot_compare_effect.py
src/gwaslab/viz/viz_plot_credible_sets.py
src/gwaslab/viz/viz_plot_density.py
src/gwaslab/viz/viz_plot_density_mode.py
src/gwaslab/viz/viz_plot_effect.py
src/gwaslab/viz/viz_plot_forestplot.py
src/gwaslab/viz/viz_plot_ld_block.py
src/gwaslab/viz/viz_plot_ld_link.py
src/gwaslab/viz/viz_plot_manhattan_like.py
src/gwaslab/viz/viz_plot_manhattan_mode.py
src/gwaslab/viz/viz_plot_miamiplot2.py
src/gwaslab/viz/viz_plot_mqqplot.py
src/gwaslab/viz/viz_plot_phe_heatmap.py
src/gwaslab/viz/viz_plot_phenogram.py
src/gwaslab/viz/viz_plot_qqplot.py
src/gwaslab/viz/viz_plot_regional2.py
src/gwaslab/viz/viz_plot_rg_heatmap.py
src/gwaslab/viz/viz_plot_scatter_with_reg.py
src/gwaslab/viz/viz_plot_stackedpanel.py
src/gwaslab/viz/viz_plot_stackedregional.py
src/gwaslab/viz/viz_plot_template.py
src/gwaslab/viz/viz_plot_track.py
src/gwaslab/viz/viz_plot_trumpetplot.py
test/test_chromosome_mapper.py
test/test_chromosome_mapper_reference_formats.py
test/test_cli.py
test/test_clumping.py
test/test_fill_data.py
test/test_filter_bed.py
test/test_fix_id_comprehensive.py
test/test_get_lead_top.py
test/test_get_proxy.py
test/test_get_signal_density.py
test/test_gsf_io.py
test/test_gwascatalog.py
test/test_gwaslab_harmoniser_consistency.py
test/test_highlight_pinpoint.py
test/test_infer_build_and_hapmap3.py
test/test_io_to_formats.py
test/test_ldsc.py
test/test_liftover.py
test/test_meta_analyze_consistency.py
test/test_meta_analyze_metal.py
test/test_meta_analyze_multi.py
test/test_meta_analyze_polars.py
test/test_meta_regress_mrmega.py
test/test_multisusie_rss.py
test/test_path_manager.py
test/test_preformat_input.py
test/test_process_plink_input_files.py
test/test_qc_and_harmonize.py
test/test_qc_normalize_region.py
test/test_r_runner.py
test/test_read_ldsc_plot_rg.py
test/test_report.py
test/test_rsid_to_chrpos_hdf5.py
test/test_simulate_sumstats.py
test/test_sumstats_chaining.py
test/test_sumstats_filters_and_search.py
test/test_sumstats_multi_keep_all_variants.py
test/test_sumstats_object.py
test/test_sumstats_pair.py
test/test_sumstats_set.py
test/test_target_sumstats_qc.py
test/test_tutorial_v4.py
test/test_util_ex_calculate_ldmatrix.py
test/test_validate_ssf.py
test/test_validate_ssf_comprehensive.py
test/test_viz_compare_effect.py
test/test_viz_ld_block.py
test/test_viz_ld_link.py
test/test_viz_mqqplot.py
test/test_viz_panel.py
test/test_viz_params_manager.py
test/test_viz_related_plots.py