LICENSE.txt
MANIFEST.in
README.md
setup.py
mspypeline/__init__.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_default.yml
mspypeline/config/go_terms/ACTIN.txt
mspypeline/config/go_terms/BIOCARTA_EGF_PATHWAY.txt
mspypeline/config/go_terms/BIOCARTA_EPO_PATHWAY.txt
mspypeline/config/go_terms/BIOCARTA_TGFB_PATHWAY.txt
mspypeline/config/go_terms/CELL JUNCTION + ANCHORING JUNCTION + GAP JUNCTION + ADHERENS JUNCTION + TIGHT JUNCTION.txt
mspypeline/config/go_terms/CELL PROJECTION.txt
mspypeline/config/go_terms/CENTROSOME + CENTRIOLE.txt
mspypeline/config/go_terms/CYTOPLASM.txt
mspypeline/config/go_terms/CYTOPLASMIC VESICLE.txt
mspypeline/config/go_terms/CYTOSKELETON.txt
mspypeline/config/go_terms/CYTOSOL.txt
mspypeline/config/go_terms/ENDOPLASMIC RETICULUM.txt
mspypeline/config/go_terms/ENDOSOME + ENDOSOMAL.txt
mspypeline/config/go_terms/EXTRACELLULAR.txt
mspypeline/config/go_terms/GOLGI.txt
mspypeline/config/go_terms/GO_APOPTOTIC_SIGNALING_PATHWAY.txt
mspypeline/config/go_terms/GO_CYTOKINE_PRODUCTION.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_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION.txt
mspypeline/config/go_terms/GO_RESPONSE_TO_HEPATOCYTE_GROWTH_FACTOR.txt
mspypeline/config/go_terms/GO_Regeneration.txt
mspypeline/config/go_terms/LIPID DROPLET.txt
mspypeline/config/go_terms/LYSOSOME + LYSOSOMAL.txt
mspypeline/config/go_terms/MICROTUBULE.txt
mspypeline/config/go_terms/MITOCHONDRION + MITOCHONDRIAL.txt
mspypeline/config/go_terms/NABA_MATRISOME.txt
mspypeline/config/go_terms/NABA_MATRISOME_ASSOCIATED.txt
mspypeline/config/go_terms/NUCLEUS + NUCLEAR + NUCLEOLUS + NUCLEOLAR.txt
mspypeline/config/go_terms/PERIPLASM.txt
mspypeline/config/go_terms/PEROXISOME.txt
mspypeline/config/go_terms/PLASMA MEMBRANE.txt
mspypeline/config/go_terms/REACTOME_MET_RECEPTOR_ACTIVATION.txt
mspypeline/config/go_terms/RIBOSOME.txt
mspypeline/config/go_terms/THYLAKOID.txt
mspypeline/config/go_terms/VACUOLE.txt
mspypeline/config/pathways/BIOCARTA_EGF_PATHWAY.txt
mspypeline/config/pathways/BIOCARTA_EPO_PATHWAY.txt
mspypeline/config/pathways/BIOCARTA_INFLAM_PATHWAY.txt
mspypeline/config/pathways/BIOCARTA_TGFB_PATHWAY.txt
mspypeline/config/pathways/CUSTOM_AXL_PATHWAY.txt
mspypeline/config/pathways/GO_APOPTOTIC_SIGNALING_PATHWAY.txt
mspypeline/config/pathways/GO_CYTOKINE_PRODUCTION.txt
mspypeline/config/pathways/GO_INFLAMMATORY_RESPONSE.txt
mspypeline/config/pathways/GO_NEGATIVE_REGULATION_OF_INFLAMMATORY_RESPONSE.txt
mspypeline/config/pathways/GO_POSITIVE_REGULATION_OF_CYTOKINE_PRODUCTION.txt
mspypeline/config/pathways/GO_RESPONSE_TO_HEPATOCYTE_GROWTH_FACTOR.txt
mspypeline/config/pathways/GO_Regeneration.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/config/pathways/NABA_MATRISOME.txt
mspypeline/config/pathways/NABA_MATRISOME_ASSOCIATED.txt
mspypeline/config/pathways/NABA_SECRETED_FACTORS.txt
mspypeline/config/pathways/REACTOME_MET_RECEPTOR_ACTIVATION.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