├── .gitattributes ├── .github └── workflows │ ├── sagepy-connector-publish.yml │ └── sagepy-publish.yml ├── .gitignore ├── LICENSE ├── README.md ├── qfdrust ├── Cargo.toml └── src │ ├── dataset.rs │ ├── intensity.rs │ ├── lib.rs │ ├── main.rs │ ├── picked.rs │ ├── psm.rs │ └── utility.rs ├── sagepy-connector ├── .idea │ ├── .gitignore │ ├── modules.xml │ ├── sagepy-connector.iml │ └── vcs.xml ├── Cargo.lock ├── Cargo.toml └── src │ ├── lib.rs │ ├── py_database.rs │ ├── py_enzyme.rs │ ├── py_fasta.rs │ ├── py_fdr.rs │ ├── py_intensity.rs │ ├── py_ion_series.rs │ ├── py_lfq.rs │ ├── py_mass.rs │ ├── py_mobility_model.rs │ ├── py_modification.rs │ ├── py_peptide.rs │ ├── py_qfdr.rs │ ├── py_retention_alignment.rs │ ├── py_retention_model.rs │ ├── py_scoring.rs │ ├── py_spectrum.rs │ ├── py_tmt.rs │ ├── py_unimod.rs │ ├── py_utility.rs │ └── utilities.rs ├── sagepy ├── README.md ├── examples │ ├── lfq │ │ ├── LFQ.ipynb │ │ └── helpers.py │ ├── property-prediction │ │ └── property_prediction.ipynb │ ├── readme │ │ └── readme_example.ipynb │ ├── rescoring │ │ ├── bayesian_and_frequentist_rescoring.ipynb │ │ ├── data │ │ │ └── psm_data.csv │ │ └── rescoring.ipynb │ ├── sage-fdr │ │ └── FDRControl.ipynb │ └── scoring │ │ └── scoring.ipynb ├── pyproject.toml ├── sagepy │ ├── __init__.py │ ├── core │ │ ├── __init__.py │ │ ├── database.py │ │ ├── enzyme.py │ │ ├── fasta.py │ │ ├── fdr.py │ │ ├── ion_series.py │ │ ├── lfq.py │ │ ├── mass.py │ │ ├── ml │ │ │ ├── __init__.py │ │ │ ├── mobility_model.py │ │ │ ├── pep.py │ │ │ ├── retention_alignment.py │ │ │ └── retention_model.py │ │ ├── modification.py │ │ ├── peptide.py │ │ ├── scoring.py │ │ ├── spectrum.py │ │ ├── tmt.py │ │ └── unimod.py │ ├── qfdr │ │ ├── __init__.py │ │ └── tdc.py │ ├── rescore │ │ ├── __init__.py │ │ ├── lda.py │ │ ├── rescore.py │ │ ├── rt_predictor.py │ │ └── utility.py │ └── utility.py └── sagepy_logo.png └── unimod ├── Cargo.toml └── src ├── lib.rs └── unimod ├── 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