CHANGELOG.md
LICENSE
MANIFEST.in
README.md
pyproject.toml
docs/README.md
docs/api_reference.md
docs/bayes_loco_gwas_spec.md
docs/gwas_sorghum_tutorial.ipynb
docs/output_files.md
docs/quickstart.md
docs/images/farmcpu_comparison_plots.png
docs/images/trait3_methods_comparison.png
examples/01_basic_gwas.py
examples/02_mlm_with_structure.py
examples/04_with_covariates.py
examples/05_reading_results.py
examples/06_farmcpu_resampling.py
examples/EXAMPLE_DATA.md
examples/README.md
examples/example_covariates.csv
examples/example_phenotypes.csv
panicle/__init__.py
panicle/py.typed
panicle.egg-info/PKG-INFO
panicle.egg-info/SOURCES.txt
panicle.egg-info/dependency_links.txt
panicle.egg-info/entry_points.txt
panicle.egg-info/requires.txt
panicle.egg-info/top_level.txt
panicle/association/__init__.py
panicle/association/blink.py
panicle/association/farmcpu.py
panicle/association/farmcpu_resampling.py
panicle/association/glm.py
panicle/association/glm_fwl_qr.py
panicle/association/lrt.py
panicle/association/mlm.py
panicle/association/mlm_loco.py
panicle/association/bayes_loco/__init__.py
panicle/association/bayes_loco/api.py
panicle/association/bayes_loco/config.py
panicle/association/bayes_loco/data.py
panicle/association/bayes_loco/diagnostics.py
panicle/association/bayes_loco/engine.py
panicle/association/bayes_loco/state.py
panicle/cli/__init__.py
panicle/cli/utils.py
panicle/core/__init__.py
panicle/core/mvp.py
panicle/data/__init__.py
panicle/data/io_utils.py
panicle/data/load_genotype_hapmap.py
panicle/data/load_genotype_plink.py
panicle/data/load_genotype_vcf.py
panicle/data/loaders.py
panicle/matrix/__init__.py
panicle/matrix/kinship.py
panicle/matrix/kinship_loco.py
panicle/matrix/pca.py
panicle/pipelines/__init__.py
panicle/pipelines/gwas.py
panicle/tools/__init__.py
panicle/tools/convert_genotype.py
panicle/utils/__init__.py
panicle/utils/compression.py
panicle/utils/data_types.py
panicle/utils/effective_tests.py
panicle/utils/memmap_utils.py
panicle/utils/perf.py
panicle/utils/stats.py
panicle/visualization/__init__.py
panicle/visualization/manhattan.py
scripts/run_GWAS.py
tests/test_association_stats.py
tests/test_bayes_loco.py
tests/test_blink_and_farmcpu_unit.py
tests/test_blink_helpers.py
tests/test_cli_utils.py
tests/test_convert_genotype.py
tests/test_dynamic_int8_writer.py
tests/test_effective_tests.py
tests/test_farmcpu_resampling.py
tests/test_gwas_pipeline_integration.py
tests/test_load_genotype_plink_more.py
tests/test_loaders_genotype.py
tests/test_loaders_vcf_plink_hapmap.py
tests/test_loco_kinship.py
tests/test_lrt.py
tests/test_matrix_utils.py
tests/test_memmap_utils.py
tests/test_mlm_and_glm_paths.py
tests/test_mvp_core.py
tests/test_pca_additional.py
tests/test_stats_utils.py
tests/test_vcf_genotype_parsing.py
tests/test_visualization.py