.gitignore
.readthedocs.yaml
LICENSE.md
README.md
environment.yml
pyproject.toml
setup.cfg
setup.py
snakemake_env.yml
.github/workflows/ci.yaml
.github/workflows/ci_workflow.yaml
.github/workflows/test_pkg_on_colab.yaml
.github/workflows/workflow_website.yaml
docs/Makefile
docs/README.md
docs/conf.py
docs/docutils.conf
docs/environment.yml
docs/index.rst
docs/make.bat
docs/proteomics_intro.md
docs/venv_setup.md
docs/Figures/Molecular_structures_of_the_21_proteinogenic_amino_acids.svg
docs/Figures/amino_acids_iupac_iub_1983.png
docs/Figures/fig_proteomics_pipeline.png
docs/Figures/schema_orbitrap_instrument.jpg
docs/logos/logo.png
docs/logos/logo_thumbnail.png
docs/other/project_readme.rst
docs/other/tutorial.rst
pimms_learn.egg-info/PKG-INFO
pimms_learn.egg-info/SOURCES.txt
pimms_learn.egg-info/dependency_links.txt
pimms_learn.egg-info/entry_points.txt
pimms_learn.egg-info/requires.txt
pimms_learn.egg-info/top_level.txt
project/00_5_training_data_exploration.py
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project/00_6_0_permute_data.py
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project/04_1_train_pimms_models.ipynb
project/04_1_train_pimms_models.py
project/10_0_ald_data.ipynb
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project/10_2_ald_compare_methods.ipynb
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project/bin/README.md
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project/config/README.md
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project/config/across_datasets/collab.yaml
project/config/across_datasets/config.yaml
project/config/across_datasets/dae.yaml
project/config/across_datasets/shared_splits.yaml
project/config/across_datasets/vae.yaml
project/config/alzheimer_study/README.md
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project/config/appl_ald_data/plasma/aggPeptides/config.yaml
project/config/appl_ald_data/plasma/aggPeptides/split.yaml
project/config/appl_ald_data/plasma/aggPeptides/train.yaml
project/config/appl_ald_data/plasma/grid_search/config_grid.yaml
project/config/appl_ald_data/plasma/proteinGroups/comparison.yaml
project/config/appl_ald_data/plasma/proteinGroups/config.yaml
project/config/appl_ald_data/plasma/proteinGroups/config_reps.yaml
project/config/appl_ald_data/plasma/proteinGroups/inspect_data.yaml
project/config/appl_ald_data/plasma/proteinGroups/split.yaml
project/config/appl_ald_data/plasma/proteinGroups/train_CF.yaml
project/config/appl_ald_data/plasma/proteinGroups/train_DAE.yaml
project/config/appl_ald_data/plasma/proteinGroups/train_KNN.yaml
project/config/appl_ald_data/plasma/proteinGroups/train_Median.yaml
project/config/appl_ald_data/plasma/proteinGroups/train_RSN.yaml
project/config/appl_ald_data/plasma/proteinGroups/train_VAE.yaml
project/config/appl_ald_data/plasma/proteinGroups_80perc_dataset/comparison.yaml
project/config/appl_ald_data/plasma/proteinGroups_80perc_dataset/config.yaml
project/config/appl_ald_data/plasma/proteinGroups_80perc_dataset/split.yaml
project/config/grid_search_large_data/config_grid.yaml
project/config/grid_search_large_data/config_grid_small.yaml
project/config/grid_search_large_data/evidence_split.yaml
project/config/grid_search_large_data/peptides_split.yaml
project/config/grid_search_large_data/proteinGroups_split.yaml
project/config/grid_search_small_data/config_grid.yaml
project/config/grid_search_small_data/evidence_split.yaml
project/config/grid_search_small_data/peptides_split.yaml
project/config/grid_search_small_data/proteinGroups_split.yaml
project/config/knn_comparison/ald_pgs_all/README.md
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project/config/knn_comparison/hela_pgs_large/README.md
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project/config/knn_comparison/hela_pgs_large/inspect_data.yaml
project/config/knn_comparison/hela_pgs_large/split.yaml
project/config/permuted_dataset/config.yaml
project/config/permuted_dataset/split.yaml
project/config/repeat_best/split.yaml
project/config/repeat_best/train.yaml
project/config/single_dev_dataset/evidence/config.yaml
project/config/single_dev_dataset/evidence/split.yaml
project/config/single_dev_dataset/evidence/train_CF.yaml
project/config/single_dev_dataset/evidence/train_DAE.yaml
project/config/single_dev_dataset/evidence/train_KNN.yaml
project/config/single_dev_dataset/evidence/train_Median.yaml
project/config/single_dev_dataset/evidence/train_VAE.yaml
project/config/single_dev_dataset/evidence_N50/config.yaml
project/config/single_dev_dataset/evidence_N50/split.yaml
project/config/single_dev_dataset/evidence_N50/train_CF.yaml
project/config/single_dev_dataset/evidence_N50/train_DAE.yaml
project/config/single_dev_dataset/evidence_N50/train_KNN.yaml
project/config/single_dev_dataset/evidence_N50/train_Median.yaml
project/config/single_dev_dataset/evidence_N50/train_VAE.yaml
project/config/single_dev_dataset/example/config.yaml
project/config/single_dev_dataset/example/split.yaml
project/config/single_dev_dataset/example/train_CF.yaml
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project/config/single_dev_dataset/example/train_Median.yaml
project/config/single_dev_dataset/example/train_RSN.yaml
project/config/single_dev_dataset/example/train_VAE.yaml
project/config/single_dev_dataset/mnar_mcar/evi_l.yaml
project/config/single_dev_dataset/mnar_mcar/evi_m.yaml
project/config/single_dev_dataset/mnar_mcar/pep_l.yaml
project/config/single_dev_dataset/mnar_mcar/pep_m.yaml
project/config/single_dev_dataset/mnar_mcar/pg_l.yaml
project/config/single_dev_dataset/mnar_mcar/pg_m.yaml
project/config/single_dev_dataset/peptides/config.yaml
project/config/single_dev_dataset/peptides/split.yaml
project/config/single_dev_dataset/peptides/train_CF.yaml
project/config/single_dev_dataset/peptides/train_DAE.yaml
project/config/single_dev_dataset/peptides/train_KNN.yaml
project/config/single_dev_dataset/peptides/train_Median.yaml
project/config/single_dev_dataset/peptides/train_VAE.yaml
project/config/single_dev_dataset/peptides_N50/config.yaml
project/config/single_dev_dataset/peptides_N50/split.yaml
project/config/single_dev_dataset/peptides_N50/train_CF.yaml
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project/config/single_dev_dataset/peptides_N50/train_Median.yaml
project/config/single_dev_dataset/peptides_N50/train_VAE.yaml
project/config/single_dev_dataset/proteinGroups/config.yaml
project/config/single_dev_dataset/proteinGroups/inspect_data.yaml
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project/config/single_dev_dataset/proteinGroups/train_CF.yaml
project/config/single_dev_dataset/proteinGroups/train_DAE.yaml
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project/config/single_dev_dataset/proteinGroups/train_Median.yaml
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project/config/single_dev_dataset/proteinGroups_N50/config_v2.yaml
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project/config/single_dev_dataset/proteinGroups_N50/train_CF.yaml
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project/config/single_dev_dataset/proteinGroups_N50/train_Median.yaml
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project/data/README.md
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project/data/ALD_study/README.md
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project/workflow/TestNotebooks.smk
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