LICENSE
README.md
setup.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
src/pgptracker/stage2_analysis/pipeline_st2.py
src/pgptracker/stage2_analysis/plot_funcs.py
src/pgptracker/stage2_analysis/statistics.py
src/pgptracker/stage2_analysis/visualizations.py
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
src/pgptracker/wrappers/picrust/place_seqs.py
src/pgptracker/wrappers/qiime/__init__.py
src/pgptracker/wrappers/qiime/classify.py
src/pgptracker/wrappers/qiime/export_module.py