AUTHORS.rst
HISTORY.rst
LICENSE
MANIFEST.in
README.rst
setup.cfg
setup.py
docs/Makefile
docs/authors.rst
docs/conf.py
docs/history.rst
docs/index.rst
docs/installation.rst
docs/make.bat
docs/modules.rst
docs/phenotrex.cli.rst
docs/phenotrex.io.rst
docs/phenotrex.ml.clf.rst
docs/phenotrex.ml.rst
docs/phenotrex.rst
docs/phenotrex.structure.rst
docs/phenotrex.transforms.rst
docs/phenotrex.util.rst
docs/readme.rst
docs/usage.rst
phenotrex/__init__.py
phenotrex.egg-info/PKG-INFO
phenotrex.egg-info/SOURCES.txt
phenotrex.egg-info/dependency_links.txt
phenotrex.egg-info/entry_points.txt
phenotrex.egg-info/not-zip-safe
phenotrex.egg-info/requires.txt
phenotrex.egg-info/top_level.txt
phenotrex/bin/prodigal.linux
phenotrex/bin/prodigal.osx.10.9.5
phenotrex/bin/prodigal.windows.exe
phenotrex/cli/__init__.py
phenotrex/cli/cccv.py
phenotrex/cli/clf_opt.py
phenotrex/cli/compute_genotype.py
phenotrex/cli/cv.py
phenotrex/cli/generic_func.py
phenotrex/cli/generic_opt.py
phenotrex/cli/get_weights.py
phenotrex/cli/main.py
phenotrex/cli/plot.py
phenotrex/cli/predict.py
phenotrex/cli/train.py
phenotrex/io/__init__.py
phenotrex/io/flat.py
phenotrex/io/serialization.py
phenotrex/ml/__init__.py
phenotrex/ml/cccv.py
phenotrex/ml/feature_select.py
phenotrex/ml/prediction.py
phenotrex/ml/shap_handler.py
phenotrex/ml/trex_classifier.py
phenotrex/ml/vectorizer.py
phenotrex/ml/clf/__init__.py
phenotrex/ml/clf/svm.py
phenotrex/ml/clf/xgbm.py
phenotrex/structure/__init__.py
phenotrex/structure/records.py
phenotrex/transforms/__init__.py
phenotrex/transforms/annotation.py
phenotrex/transforms/resampling.py
phenotrex/util/__init__.py
phenotrex/util/helpers.py
phenotrex/util/logging.py
phenotrex/util/plotting.py
phenotrex/util/taxonomy.py
tests/__init__.py
tests/targets.py
tests/test_ml.py
tests/test_shap_handler.py
tests/test_transforms.py
tests/test_util.py
tests/test_data/Aerobe_old.genotype
tests/test_data/Aerobe_old.phenotype
tests/test_data/GCA_000692775_1_trunc2.faa
tests/test_data/GCA_000692775_1_trunc2.faa.gz
tests/test_data/GCA_000692775_1_trunc2.fna
tests/test_data/GCA_000692775_1_trunc2.fna.gz
tests/test_data/Psychro_or_tolerant.genotype
tests/test_data/Psychro_or_tolerant.phenotype
tests/test_data/Sulfate_reducer.genotype
tests/test_data/Sulfate_reducer.phenotype
tests/test_data/Sulfate_reducer.taxids
tests/test_data/Sulfate_reducer_svm.pkl
tests/test_data/Sulfate_reducer_svm_cccv.json
tests/test_data/Sulfate_reducer_xgb.pkl
tests/test_data/Sulfate_reducer_xgb_cccv.json
tests/test_data/T3SS.genotype
tests/test_data/T3SS.phenotype
tests/test_data/T3SS.taxid
tests/test_data/acetogenesis.genotype
tests/test_data/acetogenesis.phenotype
tests/test_data/svm_params.json
tests/test_data/xgb_params.json