├── .gitattributes ├── .gitignore ├── ASMS2022_Poster.pdf ├── ASMS2022_Poster.png ├── CHANGELOG.txt ├── Dockerfile ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── .nojekyll ├── Makefile └── source │ ├── _build │ └── html │ │ ├── .buildinfo │ │ ├── .doctrees │ │ ├── documentation.doctree │ │ ├── environment.pickle │ │ ├── index.doctree │ │ ├── install.doctree │ │ ├── introduction.doctree │ │ ├── license.doctree │ │ ├── to_do_list.doctree │ │ └── tutorial.doctree │ │ ├── _sources │ │ ├── documentation.rst.txt │ │ ├── index.rst.txt │ │ ├── install.rst.txt │ │ ├── introduction.rst.txt │ │ ├── license.rst.txt │ │ ├── to_do_list.rst.txt │ │ └── tutorial.rst.txt │ │ ├── _static │ │ ├── basic.css │ │ ├── css │ │ │ ├── badge_only.css │ │ │ ├── fonts │ │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ │ ├── fontawesome-webfont.eot │ │ │ │ ├── fontawesome-webfont.svg │ │ │ │ ├── fontawesome-webfont.ttf │ │ │ │ ├── fontawesome-webfont.woff │ │ │ │ ├── fontawesome-webfont.woff2 │ │ │ │ ├── lato-bold-italic.woff │ │ │ │ ├── lato-bold-italic.woff2 │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-normal-italic.woff │ │ │ │ ├── lato-normal-italic.woff2 │ │ │ │ ├── lato-normal.woff │ │ │ │ └── lato-normal.woff2 │ │ │ └── theme.css │ │ ├── doctools.js │ │ ├── documentation_options.js │ │ ├── file.png │ │ ├── fonts │ │ │ ├── FontAwesome.otf │ │ │ ├── Lato │ │ │ │ ├── lato-bold.eot │ │ │ │ ├── lato-bold.ttf │ │ │ │ ├── lato-bold.woff │ │ │ │ ├── lato-bold.woff2 │ │ │ │ ├── lato-bolditalic.eot │ │ │ │ ├── lato-bolditalic.ttf │ │ │ │ ├── lato-bolditalic.woff │ │ │ │ ├── lato-bolditalic.woff2 │ │ │ │ ├── lato-italic.eot │ │ │ │ ├── lato-italic.ttf │ │ │ │ ├── lato-italic.woff │ │ │ │ ├── lato-italic.woff2 │ │ │ │ ├── lato-regular.eot │ │ │ │ ├── lato-regular.ttf │ │ │ │ ├── lato-regular.woff │ │ │ │ └── lato-regular.woff2 │ │ │ ├── Roboto-Slab-Bold.woff │ │ │ ├── Roboto-Slab-Bold.woff2 │ │ │ ├── Roboto-Slab-Light.woff │ │ │ ├── Roboto-Slab-Light.woff2 │ │ │ ├── Roboto-Slab-Regular.woff │ │ │ ├── Roboto-Slab-Regular.woff2 │ │ │ ├── Roboto-Slab-Thin.woff │ │ │ ├── Roboto-Slab-Thin.woff2 │ │ │ ├── RobotoSlab │ │ │ │ ├── roboto-slab-v7-bold.eot │ │ │ │ ├── roboto-slab-v7-bold.ttf │ │ │ │ ├── roboto-slab-v7-bold.woff │ │ │ │ ├── roboto-slab-v7-bold.woff2 │ │ │ │ ├── roboto-slab-v7-regular.eot │ │ │ │ ├── roboto-slab-v7-regular.ttf │ │ │ │ ├── roboto-slab-v7-regular.woff │ │ │ │ └── roboto-slab-v7-regular.woff2 │ │ │ ├── fontawesome-webfont.eot │ │ │ ├── fontawesome-webfont.svg │ │ │ ├── fontawesome-webfont.ttf │ │ │ ├── fontawesome-webfont.woff │ │ │ ├── fontawesome-webfont.woff2 │ │ │ ├── lato-bold-italic.woff │ │ │ ├── lato-bold-italic.woff2 │ │ │ ├── lato-bold.woff │ │ │ ├── lato-bold.woff2 │ │ │ ├── lato-normal-italic.woff │ │ │ ├── lato-normal-italic.woff2 │ │ │ ├── lato-normal.woff │ │ │ └── lato-normal.woff2 │ │ ├── jquery-3.5.1.js │ │ ├── jquery.js │ │ ├── js │ │ │ ├── badge_only.js │ │ │ ├── html5shiv-printshiv.min.js │ │ │ ├── html5shiv.min.js │ │ │ ├── modernizr.min.js │ │ │ └── theme.js │ │ ├── language_data.js │ │ ├── minus.png │ │ ├── plus.png │ │ ├── pygments.css │ │ ├── searchtools.js │ │ ├── underscore-1.3.1.js │ │ └── underscore.js │ │ ├── documentation.html │ │ ├── genindex.html │ │ ├── index.html │ │ ├── install.html │ │ ├── introduction.html │ │ ├── license.html │ │ ├── objects.inv │ │ ├── py-modindex.html │ │ ├── search.html │ │ ├── searchindex.js │ │ ├── to_do_list.html │ │ └── tutorial.html │ ├── conf.py │ ├── documentation.rst │ ├── example_group.html │ ├── example_score.html │ ├── example_status.html │ ├── example_status.png │ ├── index.rst │ ├── install.rst │ ├── introduction.rst │ ├── license.rst │ ├── nx.html │ ├── preparing_input_data.rst │ ├── protein_inference_in_python.rst │ ├── protein_inference_logo.png │ ├── protein_inference_logo_v2.png │ └── to_do_list.rst ├── example_code └── run_example_datasets.ipynb ├── example_data ├── IPRG2016 │ ├── MixtureAB │ │ ├── percolator.decoy.psms.txt │ │ ├── percolator.log.txt │ │ ├── percolator.params.txt │ │ ├── percolator.target.psms.txt │ │ ├── reprisal.decoy.peptides.csv │ │ ├── reprisal.decoy.proteins.csv │ │ ├── reprisal.target.peptides.csv │ │ ├── reprisal.target.proteins.csv │ │ └── target_networks.p │ ├── prest_1000_random.fasta │ ├── prest_pool_a.fasta │ └── prest_pool_b.fasta ├── inputs │ ├── percolator.decoy.psms.txt │ └── percolator.target.psms.txt └── outputs │ ├── reprisal.target.peptides.csv │ ├── reprisal.target.proteins.csv │ └── target_networks.p ├── make.bat ├── packages.txt ├── pi_playground.py ├── protein_inference ├── __init__.py ├── benchmarking │ ├── __init__.py │ ├── benchmark_percolator_inference.py │ ├── benchmarking.py │ ├── entrapment_benchmark.py │ └── legacy │ │ ├── compare_maxquant_output.py │ │ ├── evaluate_protein_inference.py │ │ ├── mq_input_reprisal_runner.py │ │ ├── process_maxquant_output.py │ │ ├── process_maxquant_output_legacy.py │ │ └── process_protein_inference_output.py ├── inference │ ├── __init__.py │ ├── false_discovery_rate_calculator.py │ ├── protein_merger.py │ ├── scorers.py │ └── uniqueness_tagger.py ├── main.py ├── network_grapher.py ├── problem_network.py ├── processing │ ├── __init__.py │ ├── processed_psms.py │ ├── psms_network_generator.py │ ├── psms_network_splitter.py │ └── psms_preprocessor.py ├── protein_inference_runner.py ├── reprisal │ ├── __init__.py │ └── greedy_algorithm.py └── table_maker.py ├── readme_image.png ├── requirements.txt ├── resources ├── md_logo_low_res.png ├── new_md_logo.png └── protein_inference_logo_v2.png ├── scripts ├── acceptance.sh ├── build.sh ├── make_docs.sh ├── prepare.sh └── run_docker.sh ├── setup.py ├── table1.png ├── test_data └── output │ ├── nx.html │ ├── reprisal.target.peptides.csv │ ├── reprisal.target.proteins.csv │ └── target_networks.p └── tests ├── __init__.py ├── test_data └── test_psm.txt └── unit ├── greedy_algorithm_test.py ├── problem_network_tagger_test.py ├── problem_network_test.py ├── processed_psms_test.py ├── protein_merger_test.py ├── psms_network_generator_test.py ├── psms_network_splitter_test.py └── table_writer_test.py /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MassDynamics/protein-inference/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MassDynamics/protein-inference/HEAD/.gitignore -------------------------------------------------------------------------------- /ASMS2022_Poster.pdf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MassDynamics/protein-inference/HEAD/ASMS2022_Poster.pdf 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