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.gitattributes
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CHANGELOG.md
CITATION.cff
CODE_OF_CONDUCT.md
CONTRIBUTING.md
LICENSE
NOTICE
README.dev.md
README.md
mkdocs.yml
proposed_aiproteomics_pipeline.png
pyproject.toml
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.github/workflows/cffconvert.yml
.github/workflows/documentation.yml
.github/workflows/markdown-link-check.yml
.github/workflows/pypi.yml
aiproteomics/__init__.py
aiproteomics.egg-info/PKG-INFO
aiproteomics.egg-info/SOURCES.txt
aiproteomics.egg-info/dependency_links.txt
aiproteomics.egg-info/requires.txt
aiproteomics.egg-info/top_level.txt
aiproteomics/comparison/ComparisonPrositFrag.py
aiproteomics/comparison/__init__.py
aiproteomics/datasets/DataSetPrositFrag.py
aiproteomics/datasets/__init__.py
aiproteomics/e2e/LICENSE
aiproteomics/e2e/README.md
aiproteomics/e2e/__init__.py
aiproteomics/e2e/annotate.py
aiproteomics/e2e/constants.py
aiproteomics/e2e/match.py
aiproteomics/e2e/parse_tsv.py
aiproteomics/e2e/sanitize.py
aiproteomics/e2e/speclib_writers.py
aiproteomics/e2e/speclibgen.py
aiproteomics/e2e/tensorize.py
aiproteomics/e2e/utils.py
aiproteomics/frag/__init__.py
aiproteomics/frag/models/.gitignore
aiproteomics/frag/models/__init__.py
aiproteomics/frag/models/early_fusion_transformer.py
aiproteomics/modelgen/__init__.py
aiproteomics/modelgen/prosit1_gen.py
aiproteomics/modelgen/save_model.py
aiproteomics/modelgen/test_prosit_to_onnx.py
aiproteomics/modelgen/prosit1/__init__.py
aiproteomics/modelgen/prosit1/constants.py
aiproteomics/modelgen/prosit1/layers.py
aiproteomics/modelgen/prosit1/losses.py
aiproteomics/modelgen/prosit1/sanitize.py
aiproteomics/rt/__init__.py
aiproteomics/rt/models/__init__.py
aiproteomics/rt/models/transformer_rt.py
cli/.gitignore
cli/create.py
cli/predict.py
cli/train.py
data_exploration_notebooks/analyze_predictions.ipynb
data_exploration_notebooks/analyze_predictions.py
data_exploration_notebooks/analyze_predictions.sh
data_exploration_notebooks/predict.sh
data_exploration_notebooks/train.py
data_exploration_notebooks/trainfrag.sh
demo/README.md
demo/demo_e2e.ipynb
demo/demo_spectral_angle_comparison.ipynb
demo/example.csv
demo/model.png
demo/report_prosit_e2e.ipynb
demo/uniprot_e2e.ipynb
demo/uniprot_human_100.tsv
demo/weight_67_0.22422.hdf5
docs/index.md
docs/assets/custom.css
docs/assets/fontawesome.min.js
docs/assets/icon.png
docs/assets/solid.min.js
prosit_fragmentation/CITATIONS.bib
prosit_fragmentation/README.md
prosit_fragmentation/TAGS.txt
prosit_fragmentation/__init__.py
prosit_fragmentation/checksums.tsv
prosit_fragmentation/prosit_fragmentation_dataset_builder.py
prosit_fragmentation/prosit_fragmentation_dataset_builder_test.py
prosit_fragmentation/dummy_data/sample.hdf5
prosit_fragmentation/dummy_data/val_sample.hdf5
tests/__init__.py
tests/test_model_building.py
tests/test_spectral_lib_generation.py
tests/assets/example.csv