.gitignore
LICENSE
README.md
pyproject.toml
requirements.txt
setup.py
.github/workflows/publish.yml
examples/.gitkeep
examples/test_integration_stage2.py
examples/temp_integration_test/inputs/feature_table.tsv
examples/temp_integration_test/inputs/metadata.tsv
examples/temp_integration_test/outputs/diversity/alpha_diversity.tsv
examples/temp_integration_test/outputs/diversity/alpha_observed_features.pdf
examples/temp_integration_test/outputs/diversity/alpha_observed_features.png
examples/temp_integration_test/outputs/diversity/alpha_pielou_e.pdf
examples/temp_integration_test/outputs/diversity/alpha_pielou_e.png
examples/temp_integration_test/outputs/diversity/alpha_shannon.pdf
examples/temp_integration_test/outputs/diversity/alpha_shannon.png
examples/temp_integration_test/outputs/diversity/alpha_simpson.pdf
examples/temp_integration_test/outputs/diversity/alpha_simpson.png
examples/temp_integration_test/outputs/diversity/pca_plot.pdf
examples/temp_integration_test/outputs/diversity/pca_plot.png
examples/temp_integration_test/outputs/diversity/pca_scores.tsv
examples/temp_integration_test/outputs/diversity/permanova_results.txt
examples/temp_integration_test/outputs/diversity/tsne_plot.pdf
examples/temp_integration_test/outputs/diversity/tsne_plot.png
examples/temp_integration_test/outputs/diversity/tsne_scores.tsv
examples/temp_integration_test/outputs/machine_learning/boruta_selection.tsv
examples/temp_integration_test/outputs/machine_learning/random_forest_importance.tsv
examples/temp_integration_test/outputs/machine_learning/rf_importance.pdf
examples/temp_integration_test/outputs/machine_learning/rf_importance.png
examples/temp_integration_test/outputs/normalization/clr_wide_D_N_split_data
examples/temp_integration_test/outputs/normalization/clr_wide_N_D_data
examples/temp_integration_test/outputs/normalization/raw_wide_N_D_data
examples/temp_integration_test/outputs/statistics/differential_abundance_results.tsv
examples/temp_integration_test/outputs/statistics/heatmap_significant.pdf
examples/temp_integration_test/outputs/statistics/heatmap_significant.png
examples/temp_integration_test/outputs/statistics/volcano_plot.pdf
examples/temp_integration_test/outputs/statistics/volcano_plot.png
src/__init__.py
src/pgptracker/__init__.py
src/pgptracker.egg-info/PKG-INFO
src/pgptracker.egg-info/SOURCES.txt
src/pgptracker.egg-info/dependency_links.txt
src/pgptracker.egg-info/entry_points.txt
src/pgptracker.egg-info/requires.txt
src/pgptracker.egg-info/top_level.txt
src/pgptracker/cli/__init__.py
src/pgptracker/cli/__main__.py
src/pgptracker/cli/cli.py
src/pgptracker/cli/interactive.py
src/pgptracker/cli/subcommands.py
src/pgptracker/databases/pathways_plabase.txt
src/pgptracker/environments/picrust2.yml
src/pgptracker/environments/qiime2-amplicon-2025.10.yml
src/pgptracker/stage1_processing/__init__.py
src/pgptracker/stage1_processing/gen_ko_abun.py
src/pgptracker/stage1_processing/merge_tax_abun.py
src/pgptracker/stage1_processing/pipeline_st1.py
src/pgptracker/stage1_processing/strat_pgpt.py
src/pgptracker/stage1_processing/unstrat_pgpt.py
src/pgptracker/stage2_analysis/__init__.py
src/pgptracker/stage2_analysis/clr_normalize.py
src/pgptracker/stage2_analysis/clustering_ML.py
src/pgptracker/stage2_analysis/diversity.py
src/pgptracker/stage2_analysis/ordination.py
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src/pgptracker/stage2_analysis/plot_funcs.py
src/pgptracker/stage2_analysis/statistics.py
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src/pgptracker/utils/__init__.py
src/pgptracker/utils/env_manager.py
src/pgptracker/utils/validator.py
src/pgptracker/utils/profiling_tools/__init__.py
src/pgptracker/utils/profiling_tools/profile_config.py
src/pgptracker/utils/profiling_tools/profile_reporter.py
src/pgptracker/utils/profiling_tools/profiler.py
src/pgptracker/wrappers/__init__.py
src/pgptracker/wrappers/picrust/__init__.py
src/pgptracker/wrappers/picrust/hsp_prediction.py
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src/pgptracker/wrappers/qiime/__init__.py
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src/pgptracker/wrappers/qiime/export_module.py
tests/__init__.py
tests/conftest.py
tests/comparisons/check_clr.py
tests/comparisons/clr_Normalize_debug.py
tests/comparisons/strat_pgpt_debug.py
tests/comparisons/test_p2_and_gen_ko.py
tests/comparisons/verify_stats.py
tests/unit/__init__.py
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tests/unit/test_diversity.py
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tests/unit/test_hsp_prediction.py
tests/unit/test_interactive.py
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tests/unit/test_profile_config.py
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tests/unit/test_qiime_export.py
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tests/unit/test_validators.py