MANIFEST.in
README.md
setup.py
mspypeline/__init__.py
mspypeline/__main__.py
mspypeline/version.py
mspypeline.egg-info/PKG-INFO
mspypeline.egg-info/SOURCES.txt
mspypeline.egg-info/dependency_links.txt
mspypeline.egg-info/requires.txt
mspypeline.egg-info/top_level.txt
mspypeline/config/ms_analysis_adjustable_options.yml
mspypeline/config/ms_analysis_default.yml
mspypeline/config/go_terms/GO_APOPTOTIC_SIGNALING_PATHWAY.txt
mspypeline/config/go_terms/GO_CYTOKINE_PRODUCTION.txt
mspypeline/config/go_terms/GO_EPITHELIAL_TO_MESENCHYMAL_TRANSITION.txt
mspypeline/config/go_terms/GO_EXTRACELLULAR_MATRIX.txt
mspypeline/config/go_terms/GO_GROWTH.txt
mspypeline/config/go_terms/GO_IMMUNE_RECEPTOR_ACTIVITY.txt
mspypeline/config/go_terms/GO_INFLAMMATORY_RESPONSE.txt
mspypeline/config/go_terms/GO_NEGATIVE_REGULATION_OF_INFLAMMATORY_RESPONSE.txt
mspypeline/config/go_terms/GO_NUCLEUS_LOCALIZATION.txt
mspypeline/config/go_terms/GO_PLASMA_MEMBRANE_REGION.txt
mspypeline/config/go_terms/GO_POSITIVE_REGULATION_OF_TRANSFORMING_GROWTH_FACTOR_BETA_PRODUCTION.txt
mspypeline/config/go_terms/GO_POSITIVE_REGULATION_OF_WNT_SIGNALING_PATHWAY.txt
mspypeline/config/go_terms/GO_REGENERATION.txt
mspypeline/config/pathways/BIOCARTA_EGF_PATHWAY.txt
mspypeline/config/pathways/BIOCARTA_EPO_PATHWAY.txt
mspypeline/config/pathways/BIOCARTA_TGFB_PATHWAY.txt
mspypeline/config/pathways/HALLMARK_APOPTOSIS.txt
mspypeline/config/pathways/HALLMARK_BILE_ACID_METABOLISM.txt
mspypeline/config/pathways/HALLMARK_CHOLESTEROL_HOMEOSTASIS.txt
mspypeline/config/pathways/HALLMARK_DNA_REPAIR.txt
mspypeline/config/pathways/HALLMARK_FATTY_ACID_METABOLISM.txt
mspypeline/config/pathways/HALLMARK_IL2_STAT5_SIGNALING.txt
mspypeline/config/pathways/HALLMARK_IL6_JAK_STAT3_SIGNALING.txt
mspypeline/config/pathways/HALLMARK_INFLAMMATORY_RESPONSE.txt
mspypeline/config/pathways/HALLMARK_INTERFERON_ALPHA_RESPONSE.txt
mspypeline/config/pathways/HALLMARK_INTERFERON_GAMMA_RESPONSE.txt
mspypeline/config/pathways/HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY.txt
mspypeline/core/MSPInitializer.py
mspypeline/core/MSPypeline.py
mspypeline/core/__init__.py
mspypeline/core/MSPPlots/BasePlotter.py
mspypeline/core/MSPPlots/MaxQuantPlotter.py
mspypeline/core/MSPPlots/__init__.py
mspypeline/file_reader/BaseReader.py
mspypeline/file_reader/MQReader.py
mspypeline/file_reader/__init__.py
mspypeline/flask_scripts/__init__.py
mspypeline/flask_scripts/login_db.py
mspypeline/flask_scripts/blueprints/__init__.py
mspypeline/flask_scripts/blueprints/analysis_page.py
mspypeline/flask_scripts/blueprints/register_analysis.py
mspypeline/helpers/Logger.py
mspypeline/helpers/Utils.py
mspypeline/helpers/__init__.py
mspypeline/modules/DataStructure.py
mspypeline/modules/Normalization.py
mspypeline/modules/__init__.py
mspypeline/plotting_backend/__init__.py
mspypeline/plotting_backend/matplotlib_plots.py
mspypeline/plotting_backend/plotly_plots.py
test/__init__.py
test/conftest.py
test/mock_data.py
test/test_imports.py
test/test_mock_run.py
test/test_version.py
test/core/__init__.py
test/core/test_MSPInitializer.py
test/helpers/__init__.py
test/helpers/test_Logger.py
test/helpers/test_Utils.py
test/modules/__init__.py
test/modules/test_DataStructure.py
test/modules/test_Normalization.py