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Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# EndotypY\n\nA short description of your package.\n\n## Installation\n\n```sh\n#clone git repo and navigate to directory containing the setup.py file\npip install .\n\n#or run this command in your jupyter notebook\n!pip install git+https://github.com/menchelab/EndotypY.git\n```\n\n## Documentation\n\n[View the full documentation here](https://menchelab.github.io/EndotypY/)\n\n## Usage\n\n#### import\n```python\nimport EndotypY as edy\n```\n\n#### create endotyper object and read in network and seed genes\n```python\nendo = edy.Endotyper()\n\npath_network = \u003cpath_to_network_file.tsv\u003e\npath_seed = \u003cpath_to_seed_file.txt\u003e\n\nendo.import_network(path_network)\nendo.import_seeds(path_seed)\n```\n\n#### prepare RWR\n```python\nendo.prepare_rwr(r=0.8)\n\n```\n\n#### explore the seed clusters\n```python\n#k is the size of the neighborhoods to explore\nendo.explore_seed_clusters(scaling=True, k=50)\n```\n\n#### extract a connected disease module based on seeds\n```python\nendo.extract_disease_module(seed_cluster_id = None, scaling=True, k=200)\n```\n\n#### explore the local neighborhood around all seeds\n```python\nendo.define_local_neighborhood(scaling=True, neighbor_percentage=1)\n```\n\n#### annotate the local neighborhoods with gene set enrichment\n```python\nendo.annotate_local_neighborhood(enrichr_lib='GO_Biological_Process_2023',\n                                 organism='Human',\n                                 sig_threshold=0.05)\n```\n\n#### find endotypes\n```python\nendo.define_endotypes()\n```\n\n#### visualise a single endotype\n```python\nendo.plot_endotype(iteration=1, cluster_id=2, node_size='betweenness', path_length=3)\n```\n\n\n#### visualize the network\n\n```python\nendo.visualize_network()\n```\n\n![alt text](image.png)\n\n\n#### visualize all endotypes\n```python\nendo.plot_multiple_endotypes(node_size='degree', path_length=2)\n```\n![alt text](image-1.png)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmenchelab%2Fendotypy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmenchelab%2Fendotypy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmenchelab%2Fendotypy/lists"}