LICENSE
MANIFEST.in
README.rst
pyproject.toml
setup.cfg
setup.py
src/ms_deisotope/__init__.py
src/ms_deisotope/averagine.py
src/ms_deisotope/config.py
src/ms_deisotope/constants.py
src/ms_deisotope/envelope_statistics.py
src/ms_deisotope/peak_set.py
src/ms_deisotope/plot.py
src/ms_deisotope/processor.py
src/ms_deisotope/scoring.py
src/ms_deisotope/spectrum_graph.py
src/ms_deisotope/utils.py
src/ms_deisotope/version.py
src/ms_deisotope.egg-info/PKG-INFO
src/ms_deisotope.egg-info/SOURCES.txt
src/ms_deisotope.egg-info/dependency_links.txt
src/ms_deisotope.egg-info/entry_points.txt
src/ms_deisotope.egg-info/not-zip-safe
src/ms_deisotope.egg-info/requires.txt
src/ms_deisotope.egg-info/top_level.txt
src/ms_deisotope/_c/__init__.py
src/ms_deisotope/_c/averagine.c
src/ms_deisotope/_c/averagine.pxd
src/ms_deisotope/_c/averagine.pyx
src/ms_deisotope/_c/compat.h
src/ms_deisotope/_c/compat.pxd
src/ms_deisotope/_c/deconvoluter_base.c
src/ms_deisotope/_c/deconvoluter_base.pxd
src/ms_deisotope/_c/deconvoluter_base.pyx
src/ms_deisotope/_c/peak_set.c
src/ms_deisotope/_c/peak_set.pxd
src/ms_deisotope/_c/peak_set.pyx
src/ms_deisotope/_c/scoring.c
src/ms_deisotope/_c/scoring.pxd
src/ms_deisotope/_c/scoring.pyx
src/ms_deisotope/_c/similarity_methods.c
src/ms_deisotope/_c/similarity_methods.pyx
src/ms_deisotope/_c/spectrum_graph.c
src/ms_deisotope/_c/spectrum_graph.pxd
src/ms_deisotope/_c/spectrum_graph.pyx
src/ms_deisotope/_c/units.c
src/ms_deisotope/_c/units.pyx
src/ms_deisotope/_c/utils.c
src/ms_deisotope/_c/utils.pxd
src/ms_deisotope/_c/utils.pyx
src/ms_deisotope/_c/feature_map/__init__.py
src/ms_deisotope/_c/feature_map/dependence_network.c
src/ms_deisotope/_c/feature_map/dependence_network.pxd
src/ms_deisotope/_c/feature_map/dependence_network.pyx
src/ms_deisotope/_c/feature_map/feature_fit.c
src/ms_deisotope/_c/feature_map/feature_fit.pxd
src/ms_deisotope/_c/feature_map/feature_fit.pyx
src/ms_deisotope/_c/feature_map/feature_graph.c
src/ms_deisotope/_c/feature_map/feature_graph.pxd
src/ms_deisotope/_c/feature_map/feature_graph.pyx
src/ms_deisotope/_c/feature_map/feature_map.c
src/ms_deisotope/_c/feature_map/feature_map.pxd
src/ms_deisotope/_c/feature_map/feature_map.pyx
src/ms_deisotope/_c/feature_map/feature_processor.c
src/ms_deisotope/_c/feature_map/feature_processor.pyx
src/ms_deisotope/_c/feature_map/lcms_feature.c
src/ms_deisotope/_c/feature_map/lcms_feature.pxd
src/ms_deisotope/_c/feature_map/lcms_feature.pyx
src/ms_deisotope/_c/feature_map/profile_transform.c
src/ms_deisotope/_c/feature_map/profile_transform.pyx
src/ms_deisotope/_c/feature_map/shape_fitter.c
src/ms_deisotope/_c/feature_map/shape_fitter.pxd
src/ms_deisotope/_c/feature_map/shape_fitter.pyx
src/ms_deisotope/_c/peak_dependency_network/__init__.py
src/ms_deisotope/_c/peak_dependency_network/intervals.c
src/ms_deisotope/_c/peak_dependency_network/intervals.pxd
src/ms_deisotope/_c/peak_dependency_network/intervals.pyx
src/ms_deisotope/_c/peak_dependency_network/peak_network.c
src/ms_deisotope/_c/peak_dependency_network/peak_network.pxd
src/ms_deisotope/_c/peak_dependency_network/peak_network.pyx
src/ms_deisotope/_c/peak_dependency_network/subgraph.c
src/ms_deisotope/_c/peak_dependency_network/subgraph.pxd
src/ms_deisotope/_c/peak_dependency_network/subgraph.pyx
src/ms_deisotope/clustering/__init__.py
src/ms_deisotope/clustering/alignment.py
src/ms_deisotope/clustering/lsh.py
src/ms_deisotope/clustering/peak_clustering.py
src/ms_deisotope/clustering/scan_clustering.py
src/ms_deisotope/clustering/similarity_methods.py
src/ms_deisotope/data_source/__init__.py
src/ms_deisotope/data_source/_buffer.py
src/ms_deisotope/data_source/_compression.py
src/ms_deisotope/data_source/_thermo_helper.py
src/ms_deisotope/data_source/_threadsafe.py
src/ms_deisotope/data_source/agilent_d.py
src/ms_deisotope/data_source/common.py
src/ms_deisotope/data_source/dispatch.py
src/ms_deisotope/data_source/infer_type.py
src/ms_deisotope/data_source/masslynx.py
src/ms_deisotope/data_source/memory.py
src/ms_deisotope/data_source/mgf.py
src/ms_deisotope/data_source/mzml.py
src/ms_deisotope/data_source/mzmlb.py
src/ms_deisotope/data_source/mzxml.py
src/ms_deisotope/data_source/proxi.py
src/ms_deisotope/data_source/query.py
src/ms_deisotope/data_source/text.py
src/ms_deisotope/data_source/thermo_raw.py
src/ms_deisotope/data_source/thermo_raw_net.py
src/ms_deisotope/data_source/usi.py
src/ms_deisotope/data_source/xml_reader.py
src/ms_deisotope/data_source/_vendor/AgilentD.py
src/ms_deisotope/data_source/_vendor/MSFileReader.py
src/ms_deisotope/data_source/_vendor/__init__.py
src/ms_deisotope/data_source/_vendor/bruker_tims.py
src/ms_deisotope/data_source/_vendor/ThermoRawFileReader_3_0_41/__init__.py
src/ms_deisotope/data_source/_vendor/ThermoRawFileReader_3_0_41/Libraries/ThermoFisher.CommonCore.BackgroundSubtraction.dll
src/ms_deisotope/data_source/_vendor/ThermoRawFileReader_3_0_41/Libraries/ThermoFisher.CommonCore.Data.dll
src/ms_deisotope/data_source/_vendor/ThermoRawFileReader_3_0_41/Libraries/ThermoFisher.CommonCore.MassPrecisionEstimator.dll
src/ms_deisotope/data_source/_vendor/ThermoRawFileReader_3_0_41/Libraries/ThermoFisher.CommonCore.RawFileReader.dll
src/ms_deisotope/data_source/_vendor/ThermoRawFileReader_3_0_41/Libraries/__init__.py
src/ms_deisotope/data_source/_vendor/ThermoRawFileReader_3_0_41/License/RawFileRdr_License_Agreement_RevA.doc
src/ms_deisotope/data_source/_vendor/ThermoRawFileReader_3_0_41/License/__init__.py
src/ms_deisotope/data_source/_vendor/masslynx/MassLynxLockMassProcessor.py
src/ms_deisotope/data_source/_vendor/masslynx/MassLynxParameters.py
src/ms_deisotope/data_source/_vendor/masslynx/MassLynxRawChromatogramReader.py
src/ms_deisotope/data_source/_vendor/masslynx/MassLynxRawDefs.py
src/ms_deisotope/data_source/_vendor/masslynx/MassLynxRawInfoReader.py
src/ms_deisotope/data_source/_vendor/masslynx/MassLynxRawReader.py
src/ms_deisotope/data_source/_vendor/masslynx/MassLynxRawScanReader.py
src/ms_deisotope/data_source/_vendor/masslynx/MassLynxSampleList.py
src/ms_deisotope/data_source/_vendor/masslynx/__init__.py
src/ms_deisotope/data_source/_vendor/masslynx/libload.py
src/ms_deisotope/data_source/_vendor/masslynx/loader.py
src/ms_deisotope/data_source/metadata/__init__.py
src/ms_deisotope/data_source/metadata/activation.py
src/ms_deisotope/data_source/metadata/cv.py
src/ms_deisotope/data_source/metadata/data_transformation.py
src/ms_deisotope/data_source/metadata/file_information.py
src/ms_deisotope/data_source/metadata/instrument_components.py
src/ms_deisotope/data_source/metadata/sample.py
src/ms_deisotope/data_source/metadata/scan_traits.py
src/ms_deisotope/data_source/metadata/software.py
src/ms_deisotope/data_source/scan/__init__.py
src/ms_deisotope/data_source/scan/base.py
src/ms_deisotope/data_source/scan/loader.py
src/ms_deisotope/data_source/scan/mobility_frame.py
src/ms_deisotope/data_source/scan/proxy.py
src/ms_deisotope/data_source/scan/scan.py
src/ms_deisotope/data_source/scan/scan_iterator.py
src/ms_deisotope/deconvolution/__init__.py
src/ms_deisotope/deconvolution/api.py
src/ms_deisotope/deconvolution/averagine_based.py
src/ms_deisotope/deconvolution/base.py
src/ms_deisotope/deconvolution/composition_list.py
src/ms_deisotope/deconvolution/exhaustive.py
src/ms_deisotope/deconvolution/hybrid.py
src/ms_deisotope/deconvolution/peak_retention_strategy.py
src/ms_deisotope/deconvolution/utils.py
src/ms_deisotope/feature_map/__init__.py
src/ms_deisotope/feature_map/_mz_feature_search.py
src/ms_deisotope/feature_map/demultiplex.py
src/ms_deisotope/feature_map/dependence_network.py
src/ms_deisotope/feature_map/feature_fit.py
src/ms_deisotope/feature_map/feature_graph.py
src/ms_deisotope/feature_map/feature_map.py
src/ms_deisotope/feature_map/feature_processor.py
src/ms_deisotope/feature_map/feature_relationships.py
src/ms_deisotope/feature_map/lcms_feature.py
src/ms_deisotope/feature_map/map_viz.py
src/ms_deisotope/feature_map/mobility_frame_processor.py
src/ms_deisotope/feature_map/precursor_product_correlation.py
src/ms_deisotope/feature_map/profile_transform.py
src/ms_deisotope/feature_map/quick_index.py
src/ms_deisotope/feature_map/scan_index.py
src/ms_deisotope/feature_map/scan_interval_tree.py
src/ms_deisotope/feature_map/shape_fitter.py
src/ms_deisotope/output/__init__.py
src/ms_deisotope/output/common.py
src/ms_deisotope/output/infer_type.py
src/ms_deisotope/output/json.py
src/ms_deisotope/output/mgf.py
src/ms_deisotope/output/ms2.py
src/ms_deisotope/output/mzml.py
src/ms_deisotope/output/mzmlb.py
src/ms_deisotope/output/text.py
src/ms_deisotope/output/text_utils.py
src/ms_deisotope/peak_dependency_network/__init__.py
src/ms_deisotope/peak_dependency_network/interval_viz.py
src/ms_deisotope/peak_dependency_network/intervals.py
src/ms_deisotope/peak_dependency_network/peak_network.py
src/ms_deisotope/peak_dependency_network/subgraph.py
src/ms_deisotope/peak_dependency_network/utils.py
src/ms_deisotope/qc/__init__.py
src/ms_deisotope/qc/delta.py
src/ms_deisotope/qc/graph_reduction.py
src/ms_deisotope/qc/heuristic.py
src/ms_deisotope/qc/isolation.py
src/ms_deisotope/qc/signature.py
src/ms_deisotope/task/__init__.py
src/ms_deisotope/task/log_utils.py
src/ms_deisotope/task/task.py
src/ms_deisotope/test/__init__.py
src/ms_deisotope/test/common.py
src/ms_deisotope/tools/__init__.py
src/ms_deisotope/tools/conversion.py
src/ms_deisotope/tools/draw.py
src/ms_deisotope/tools/indexing.py
src/ms_deisotope/tools/maintenance.py
src/ms_deisotope/tools/utils.py
src/ms_deisotope/tools/view.py
src/ms_deisotope/tools/deisotoper/__init__.py
src/ms_deisotope/tools/deisotoper/collator.py
src/ms_deisotope/tools/deisotoper/main.py
src/ms_deisotope/tools/deisotoper/output.py
src/ms_deisotope/tools/deisotoper/process.py
src/ms_deisotope/tools/deisotoper/scan_generator.py
src/ms_deisotope/tools/deisotoper/workflow.py