LICENSE
README.md
pyproject.toml
src/analysis/lcms/scaling_factor.py
src/analysis/lcms/IBD/ibd_pMS2_mol_network.py
src/analysis/lcms/IBD/ihmp2_analysis.py
src/analysis/lcms/IBD/ihmp2_heatmap.py
src/analysis/lcms/IBD/ihmp2_match_to_identified_list.py
src/analysis/lcms/IBD/ihmp2_stats_analysis.py
src/analysis/lcms/IBD/ihmp2_tSNE.py
src/analysis/lcms/IBD/data/ibd_demo_ms2_fig.py
src/analysis/lcms/IBD/old/_ihmp2_upset_plot.py
src/analysis/lcms/IBD/old/_workbench_api.py
src/analysis/lcms/IBD/old/ihmp2_analysis.py
src/analysis/lcms/IBD/old/ihmp2_heatmap.py
src/analysis/lcms/IBD/old/ihmp2_match_to_identified_list.py
src/analysis/lcms/IBD/old/ihmp2_stats_analysis.py
src/analysis/lcms/IBD/old/ihmp2_umap.py
src/analysis/lcms/ms1_masst_demo/masst_demo_ms2_fig.py
src/analysis/lcms/ms1_masst_demo/ms1_masst.py
src/analysis/lcms/nist/nist_analysis.py
src/analysis/lcms/nist/nist_barplot.py
src/analysis/lcms/nist/nist_boxplot_peakHeight.py
src/analysis/lcms/nist/nist_boxplot_vertical.py
src/analysis/lcms/nist/nist_cmpd_class_scatter.py
src/analysis/lcms/nist/nist_demo_ms2_fig.py
src/analysis/lcms/nist/nist_mol_network.py
src/analysis/lcms/nist/nist_phe_C3_scatter_plot.py
src/analysis/lcms/nist/nist_spec_sim.py
src/analysis/lcms/nist/nist_structure_similarity.py
src/analysis/lcms/nist/revcos_main.py
src/analysis/lcms/nist/old/nist_analysis.py
src/analysis/lcms/nist/old/nist_annotation_bar.py
src/analysis/lcms/nist/old/nist_annotation_venn.py
src/analysis/lcms/nist/old/nist_demo_ms2_fig.py
src/analysis/lcms/nist/old/nist_demo_ms2_multi_adduct.py
src/analysis/lcms/nist/old/nist_demo_xics.py
src/analysis/lcms/nist/old/nist_feature_intensity_distribution.py
src/analysis/lcms/nist/old/nist_plot_ce.py
src/analysis/lcms/plot_all_mirror/all_ms2plot_lcms.py
src/analysis/lcms/std/_preprocess_ms2.py
src/analysis/lcms/std/choose_scale_k.py
src/analysis/lcms/std/flash_cos.py
src/analysis/lcms/std/make_library.py
src/analysis/lcms/std/std_ms2_fig.py
src/analysis/lcms/std/std_score_distribution.py
src/analysis/msi/cell/cell_analysis.py
src/analysis/msi/cell/cell_demo_ion-image.py
src/analysis/msi/cell/cell_demo_ms2.py
src/analysis/msi/mouse_body/mouse_body_analysis.py
src/analysis/msi/mouse_body/mousebody_demo_ms2.py
src/analysis/msi/mouse_body/mousebody_ion-image.py
src/analysis/msi/mouse_body/plot_all_ion_image.py
src/analysis/msi/mouse_brain/brain_merge_results.py
src/analysis/msi/mouse_brain/mtbls313_demo_ion-image.py
src/analysis/msi/mouse_brain/mtbls313_demo_ms2.py
src/analysis/msi/mouse_brain/plot_all_ion_image.py
src/analysis/msi/mouse_kidney/mousekidney_ion-image.py
src/analysis/msi/mouse_kidney/plot_all_ion_image.py
src/analysis/msi/mouse_liver/plot_all_ion_image.py
src/analysis/msi/ms_scan/msi_scan_intensity.py
src/analysis/msi/mz_cor/imaging_mz_cor.py
src/analysis/msi/plot_all_mirror/all_ms2_plot.py
src/deprecated/flash_entropy.py
src/ms1_id/__init__.py
src/ms1_id/annotate.py
src/ms1_id/cli.py
src/ms1_id.egg-info/PKG-INFO
src/ms1_id.egg-info/SOURCES.txt
src/ms1_id.egg-info/dependency_links.txt
src/ms1_id.egg-info/entry_points.txt
src/ms1_id.egg-info/requires.txt
src/ms1_id.egg-info/top_level.txt
src/ms1_id/lcms/__init__.py
src/ms1_id/lcms/annotate_adduct.py
src/ms1_id/lcms/annotate_ms2.py
src/ms1_id/lcms/calculate_ppc.py
src/ms1_id/lcms/centroid_data.py
src/ms1_id/lcms/export.py
src/ms1_id/lcms/group_ppc.py
src/ms1_id/lcms/main_lcms.py
src/ms1_id/lcms/masscube_alignment.py
src/ms1_id/lcms/masscube_peak_dection.py
src/ms1_id/lcms/masscube_raw_data_utils.py
src/ms1_id/lcms/ms1id_lcms_batch.py
src/ms1_id/lcms/ms1id_lcms_single.py
src/ms1_id/lcms/reverse_matching.py
src/ms1_id/lcms/utils.py
src/ms1_id/msi/__init__.py
src/ms1_id/msi/calculate_mz_cor_parallel.py
src/ms1_id/msi/centroid_data.py
src/ms1_id/msi/export_msi.py
src/ms1_id/msi/group_mz_cor_parallel.py
src/ms1_id/msi/main_msi.py
src/ms1_id/msi/ms1id_msi_workflow.py
src/ms1_id/msi/process_msi_data.py
src/ms1_id/msi/reverse_matching_parallel.py
src/ms1_id/msi/utils_imaging.py
src/ms1_id/search_utils/__init__.py
src/ms1_id/search_utils/flash_cos.py
src/ms1_id/search_utils/preprocess_ms2.py
src/scaling_fdr/_centroid_data.py
src/scaling_fdr/_preprocess_ms2.py
src/scaling_fdr/analyze_fdr_results.py
src/scaling_fdr/calc_mces.py
src/scaling_fdr/fdr_plots.py
src/scaling_fdr/flash_cos.py
src/scaling_fdr/prepare_qry_db.py
src/scaling_fdr/search_gnps.py