.gitattributes
.gitignore
CHANGELOG.md
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
README.md
RELEASING.md
pyproject.toml
.github/workflows/ci.yml
.github/workflows/library-env.yml
conda-recipe/README.md
conda-recipe/meta.yaml
deeptaxa/__init__.py
deeptaxa/cli.py
deeptaxa/config.py
deeptaxa/dataset.py
deeptaxa/describe.py
deeptaxa/predict.py
deeptaxa/train.py
deeptaxa/tune.py
deeptaxa/utils.py
deeptaxa/models/__init__.py
deeptaxa/models/bert.py
deeptaxa/models/cnn.py
deeptaxa/models/hybrid.py
deeptaxa/models/losses.py
deeptaxa_rrna.egg-info/PKG-INFO
deeptaxa_rrna.egg-info/SOURCES.txt
deeptaxa_rrna.egg-info/dependency_links.txt
deeptaxa_rrna.egg-info/entry_points.txt
deeptaxa_rrna.egg-info/requires.txt
deeptaxa_rrna.egg-info/scm_file_list.json
deeptaxa_rrna.egg-info/scm_version.json
deeptaxa_rrna.egg-info/top_level.txt
environment-files/deeptaxa-qiime2-amplicon-2024.10.yml
q2_deeptaxa/__init__.py
q2_deeptaxa/_checkpoint.py
q2_deeptaxa/_formats.py
q2_deeptaxa/_methods.py
q2_deeptaxa/_taxonomy.py
q2_deeptaxa/_types.py
q2_deeptaxa/_visualizers.py
q2_deeptaxa/citations.bib
q2_deeptaxa/plugin_setup.py
q2_deeptaxa/tests/__init__.py
q2_deeptaxa/tests/test_actions.py
q2_deeptaxa/tests/test_checkpoint.py
q2_deeptaxa/tests/test_plugin.py
q2_deeptaxa/tests/test_taxonomy.py
scripts/calibration_diagnosis.sh
scripts/calibration_sweep.sh
scripts/deeptaxa_workflow.sh
scripts/ensemble_predict.py
scripts/run_ablation.sh
scripts/run_amplicon_eval.sh
scripts/run_experiment.sh
scripts/run_similarity_eval.sh
scripts/sequence_similarity.py
scripts/similarity_curve.py
scripts/simulate_amplicons.py
tests/__init__.py
tests/_synth.py
tests/test_bert_pooling.py
tests/test_dataset.py
tests/test_gradient_accumulation.py
tests/test_pooling_mask.py
tests/test_predict_agreement.py
tests/test_predict_auc.py
tests/test_save_best_only.py
tests/test_train_predict_smoke.py
tutorials/.gitignore
tutorials/Makefile
tutorials/_quarto.yml
tutorials/analysis.qmd
tutorials/apa.csl
tutorials/architecture.qmd
tutorials/casestudy.qmd
tutorials/custom.scss
tutorials/ensemble.qmd
tutorials/glossary.qmd
tutorials/index.qmd
tutorials/prediction.qmd
tutorials/qiime2.qmd
tutorials/references.bib
tutorials/references.qmd
tutorials/render_tutorials.sh
tutorials/training.qmd
tutorials/validation.qmd
tutorials/casestudy/analysis.qmd
tutorials/casestudy/gut_brain_axis.jpg
tutorials/casestudy/social_card.jpg
tutorials/casestudy/data/asv_counts.tsv
tutorials/casestudy/data/asv_seqs.fasta
tutorials/casestudy/data/asv_taxonomy.tsv
tutorials/casestudy/data/asv_taxonomy_silva.tsv
tutorials/casestudy/data/samples.tsv
tutorials/casestudy/data/track_reads.tsv
tutorials/casestudy/pipeline/01_dada2_asv.R
tutorials/casestudy/pipeline/02_classify_silva.R
tutorials/casestudy/pipeline/README.md
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tutorials/validation/_metadata.yml
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tutorials/validation/v3-v4.ipynb
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