LICENSE
MANIFEST.in
README.md
pyproject.toml
alphaquant/__init__.py
alphaquant/run_pipeline.py
alphaquant.egg-info/PKG-INFO
alphaquant.egg-info/SOURCES.txt
alphaquant.egg-info/dependency_links.txt
alphaquant.egg-info/entry_points.txt
alphaquant.egg-info/requires.txt
alphaquant.egg-info/top_level.txt
alphaquant/benchm/__init__.py
alphaquant/benchm/benchmarking.py
alphaquant/benchm/ratios.py
alphaquant/benchm/sensitivity.py
alphaquant/classify/__init__.py
alphaquant/classify/classification_utils.py
alphaquant/classify/classify_fragments.py
alphaquant/classify/classify_precursors.py
alphaquant/classify/ml_info_table.py
alphaquant/classify/training_functions.py
alphaquant/cluster/__init__.py
alphaquant/cluster/cluster_ions.py
alphaquant/cluster/cluster_missingval.py
alphaquant/cluster/cluster_sorting.py
alphaquant/cluster/cluster_utils.py
alphaquant/cluster/ml_reorder.py
alphaquant/cluster/outlier_scoring.py
alphaquant/cluster/proteoform_statistics.py
alphaquant/config/__init__.py
alphaquant/config/config.py
alphaquant/config/download_links_for_testfiles_quicktest.yaml
alphaquant/config/download_links_for_testfiles_selected.yaml
alphaquant/config/quant_reader_config.yaml
alphaquant/config/quant_reader_config_lightweight.yaml
alphaquant/config/spectronaut_tableconfig_fragion.rs
alphaquant/config/spectronaut_tableconfig_precursor.rs
alphaquant/config/spectronaut_tableconfig_ptm_fragion.rs
alphaquant/config/variables.py
alphaquant/diffquant/__init__.py
alphaquant/diffquant/background_distributions.py
alphaquant/diffquant/condpair_analysis.py
alphaquant/diffquant/diff_analysis.py
alphaquant/diffquant/diffutils.py
alphaquant/diffquant/doublediff_analysis.py
alphaquant/multicond/__init__.py
alphaquant/multicond/diffresults_handling.py
alphaquant/multicond/median_condition_analysis.py
alphaquant/multicond/median_condition_creation.py
alphaquant/multicond/multicond_ptmnorm.py
alphaquant/multicond/multicond_utils.py
alphaquant/norm/__init__.py
alphaquant/norm/normalization.py
alphaquant/plotting/__init__.py
alphaquant/plotting/alphamapviz.py
alphaquant/plotting/base_functions.py
alphaquant/plotting/classify.py
alphaquant/plotting/colors.py
alphaquant/plotting/fcviz.py
alphaquant/plotting/fcviz_medianref.py
alphaquant/plotting/multicond.py
alphaquant/plotting/pairwise.py
alphaquant/plotting/phospho_vs_native.py
alphaquant/plotting/tree_and_fc_viz.py
alphaquant/plotting/treeutils.py
alphaquant/plotting/treeviz.py
alphaquant/ptm/__init__.py
alphaquant/ptm/phospho_inference.py
alphaquant/ptm/protein_ptm_normalization.py
alphaquant/ptm/ptmsite_mapping.py
alphaquant/resources/__init__.py
alphaquant/resources/database_loader.py
alphaquant/resources/docs/Empty_manual.pdf
alphaquant/resources/img/github.png
alphaquant/resources/img/max-planck-gesellschaft.jpg
alphaquant/resources/img/mpi_logo.png
alphaquant/resources/img/ms_pipeline_visualization.png
alphaquant/resources/style/dashboard_style.css
alphaquant/tables/__init__.py
alphaquant/tables/alphadia_reader.py
alphaquant/tables/diffquant_table.py
alphaquant/tables/misctables.py
alphaquant/tables/proteoformtable.py
alphaquant/tables/tableutils.py
alphaquant/ui/cli.py
alphaquant/ui/dashboad_parts_plots_basic.py
alphaquant/ui/dashboard_parts_plots_proteoforms.py
alphaquant/ui/dashboard_parts_run_pipeline.py
alphaquant/ui/gui.py
alphaquant/ui/gui_textfields.py
alphaquant/utils/benchmark_utils.py
alphaquant/utils/diffquant_utils.py
alphaquant/utils/proteoform_utils.py
alphaquant/utils/reader_utils.py
alphaquant/utils/utils.py
release/pyinstaller/alphaquant_pyinstaller.py
requirements/requirements.txt
requirements/requirements_development.txt
requirements/requirements_gui.txt
requirements/requirements_gui_loose.txt
requirements/requirements_loose.txt
requirements/requirements_tests.txt
tests/download_testfiles.py
tests/pytest/test_requirements.py
tests/unit_tests/test_background_distributions.py
tests/unit_tests/test_classify_precursors.py
tests/unit_tests/test_cluster_ions.py
tests/unit_tests/test_clusterutils.py
tests/unit_tests/test_diff_analysis.py
tests/unit_tests/test_diff_condpair_analysis.py
tests/unit_tests/test_doublediff_analysis.py
tests/unit_tests/test_median_condition_creation.py
tests/unit_tests/test_median_conditon_analysis.py
tests/unit_tests/test_ml_reorder.py
tests/unit_tests/test_normalization.py
tests/unit_tests/test_protein_ptm_normalization.py
tests/unit_tests/test_proteoform_statistics.py
tests/unit_tests/test_ptmsite_mapping.py
tests/unit_tests/test_tableutils.py
tests/unit_tests/test_training_functions.py