├── .github └── workflows │ ├── build.yml │ ├── docker.yml │ ├── rust.yml │ └── upload_artifacts │ └── action.yml ├── .gitignore ├── CHANGELOG.md ├── CITATION.cff ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── Cargo.lock ├── Cargo.toml ├── DOCS.md ├── Dockerfile ├── LICENSE ├── README.md ├── crates ├── sage-cli │ ├── Cargo.toml │ ├── src │ │ ├── input.rs │ │ ├── lib.rs │ │ ├── main.rs │ │ ├── output.rs │ │ ├── runner.rs │ │ └── telemetry.rs │ └── tests │ │ └── integration.rs ├── sage-cloudpath │ ├── Cargo.toml │ └── src │ │ ├── lib.rs │ │ ├── mgf.rs │ │ ├── mzml.rs │ │ ├── parquet.rs │ │ ├── tdf.rs │ │ └── util.rs └── sage │ ├── Cargo.toml │ ├── src │ ├── database.rs │ ├── enzyme.rs │ ├── fasta.rs │ ├── fdr.rs │ ├── heap.rs │ ├── ion_series.rs │ ├── isotopes.rs │ ├── lfq.rs │ ├── lib.rs │ ├── mass.rs │ ├── ml │ │ ├── gauss.rs │ │ ├── kde.rs │ │ ├── linear_discriminant.rs │ │ ├── matrix.rs │ │ ├── mobility_model.rs │ │ ├── mod.rs │ │ ├── qvalue.rs │ │ ├── retention_alignment.rs │ │ └── retention_model.rs │ ├── modification.rs │ ├── peptide.rs │ ├── scoring.rs │ ├── spectrum.rs │ └── tmt.rs │ └── tests │ └── integration.rs ├── figures ├── SageLDA.png ├── TMT_IDs.png ├── TMT_Panel.png ├── benchmark_params │ ├── README.md │ ├── comet.open │ ├── comet.tmt │ ├── fragger.open │ ├── fragger.tmt │ ├── open.json │ └── tmt.json ├── chimera_27525.png ├── lda_comparison.png ├── logo.png └── rt_model.png └── tests ├── LQSRPAAPPAPGPGQLTLR.mzML ├── LQSRPAAPPAPGPGQLTLR.png ├── Q99536.fasta ├── config-cli.json ├── config.json └── lfq_test.json /.github/workflows/build.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/lazear/sage/HEAD/.github/workflows/build.yml -------------------------------------------------------------------------------- /.github/workflows/docker.yml: -------------------------------------------------------------------------------- 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