├── .Rprofile ├── .gitignore ├── .travis.yml ├── LICENSE ├── README.md ├── apt.txt ├── data ├── README.md ├── download.sh └── storage.zip ├── environment.yml ├── figures ├── flowchart.dio ├── flowchart.png ├── overview.pdf ├── overview.png └── repository.svg ├── helpers ├── __init__.py ├── awesome.py ├── colors.R ├── features.py ├── frames.py ├── freeze.R ├── mermaid.py ├── n_grams.py ├── parse_pubmed.py ├── plots.R ├── restore.R ├── stats.py ├── text_processing.py └── utils.py ├── manual_curation └── computational_methods │ ├── bioinformatics_journal-annotated.csv │ └── subjects-annotated.csv ├── notebooks ├── Article_types.ipynb ├── Diseases_and_datasets.ipynb ├── Exploration.ipynb ├── Feature_engineering.ipynb ├── Flowchart.ipynb ├── Journals.ipynb ├── Literature_data.ipynb ├── Omics_terms.ipynb ├── Overview.ipynb ├── Source_code.ipynb ├── notebook_setup.ipynb └── paths.py ├── omics.py ├── pipeline.py ├── renv.lock ├── renv └── activate.R ├── repository_detection.py ├── 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