├── .gitignore ├── LICENSE ├── README.md ├── code ├── bundle_to_html.py ├── collapsible_tree_v3.html ├── collapsible_tree_v3_internal_data.js ├── internalized_tables.js ├── jobs.py ├── json_ontology_extender.py ├── lib │ ├── d3.v3.min.js │ ├── d3.v6.min.js │ ├── datatables.min.css │ ├── datatables.min.js │ ├── jquery-3.6.0.min.js │ ├── jquery.dataTables.min.css │ ├── makeTable.js │ └── tree_visualizer_style.css ├── masst_batch_client.py ├── masst_client.py ├── masst_data_statistics.ipynb ├── masst_dataset_summary.py ├── masst_tree.py ├── masst_utils.py ├── prepare_check_metadata.py ├── prepare_sample_counts_tree.py ├── summary_across_metadata.ipynb ├── usi_utils.py └── utils.py ├── data ├── food_masst_table.csv ├── food_masst_table_full.tsv ├── food_masst_tree.json ├── microbe_masst_table.csv ├── microbe_masst_tree.json ├── microbiome_masst_table.tsv ├── microbiome_masst_tree.json ├── personalCareProduct_masst_table.csv ├── personalCareProduct_masst_tree.json ├── plant_masst_table.csv ├── plant_masst_table_full.csv ├── plant_masst_tree.json ├── tissue_masst_table.csv ├── tissue_masst_table_full.csv └── tissue_masst_tree.json ├── examples ├── empty.mgf ├── example_careproduct.csv ├── example_links.tsv ├── example_links2.tsv ├── example_links3.tsv ├── example_links5.csv ├── example_links6.csv ├── input_spectra.mgf ├── plant_masst_examples.tsv ├── small.mgf └── wender_plants.csv ├── requirements.txt ├── tests └── fast_masst_test.py └── trees ├── microbe_masst_tree ├── .ipynb_checkpoints │ └── microbemasst_tree_generator-checkpoint.ipynb ├── Extracted_nodes_microbe.csv ├── list_ncbi_microbemasst.csv ├── microbe_masst_table.csv ├── microbe_masst_tree.json ├── microbemasst_tree_generator.R ├── microbemasst_tree_generator.ipynb ├── microbemasst_tree_raw.json ├── microbemasst_tree_raw.nw ├── microbemasst_tree_trimmed.nw └── nodes_to_remove.csv ├── microbiome_masst_tree ├── file_info.csv ├── microbiomeMASST_metadata_table.py ├── microbiomeMASST_tree_generation.py ├── tree_df.csv └── tree_df_group_size.tsv ├── personalCareProduct_masst_tree ├── personalCareProduct_FileAssoc.csv └── personalCareProduct_tree_generator.py ├── plant_masst_tree ├── .ipynb_checkpoints │ └── plantmasst_tree_generator-checkpoint.ipynb ├── Extracted_nodes_plant.csv ├── list_ncbi_plantmasst.csv ├── nodes_to_remove.csv ├── plant_masst_table.csv ├── plant_masst_tree.json ├── plantmasst_tree_generator.R ├── plantmasst_tree_generator.ipynb ├── plantmasst_tree_raw.json ├── plantmasst_tree_raw.nw └── plantmasst_tree_trimmed.nw └── tissue_masst ├── tissueMASST.R ├── tissueMASST.ipynb ├── tissue_masst_id_count.csv ├── tissue_masst_table.csv └── tissue_masst_tree.json /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/robinschmid/microbe_masst/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: 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