GitHub - chrlatte/ReCIPE

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Name		Name	Last commit message	Last commit date
Latest commit History 24 Commits
data		data
demo_data		demo_data
.gitignore		.gitignore
DEMO.ipynb		DEMO.ipynb
README		README
cluster_class.py		cluster_class.py
connectivity.ipynb		connectivity.ipynb
d1_ic100_medium.ipynb		d1_ic100_medium.ipynb
d1_ic100_small.ipynb		d1_ic100_small.ipynb
d1_ic10_medium.ipynb		d1_ic10_medium.ipynb
d1_ic10_small.ipynb		d1_ic10_small.ipynb
d1_ic50_medium.ipynb		d1_ic50_medium.ipynb
d1_ic50_small.ipynb		d1_ic50_small.ipynb
d2_ic100_medium.ipynb		d2_ic100_medium.ipynb
d2_ic100_small.ipynb		d2_ic100_small.ipynb
d2_ic10_medium.ipynb		d2_ic10_medium.ipynb
d2_ic10_small.ipynb		d2_ic10_small.ipynb
d2_ic50_medium.ipynb		d2_ic50_medium.ipynb
d2_ic50_small.ipynb		d2_ic50_small.ipynb
d3_ic100_medium.ipynb		d3_ic100_medium.ipynb
d3_ic100_small.ipynb		d3_ic100_small.ipynb
d3_ic10_medium.ipynb		d3_ic10_medium.ipynb
d3_ic10_small.ipynb		d3_ic10_small.ipynb
d3_ic50_medium.ipynb		d3_ic50_medium.ipynb
d3_ic50_small.ipynb		d3_ic50_small.ipynb
degreelist_class.py		degreelist_class.py
matrix_class.py		matrix_class.py
recipe_demo.ipynb		recipe_demo.ipynb
recipe_utils.py		recipe_utils.py
template.ipynb		template.ipynb

Repository files navigation

Required Packages:


for the classes:
    numpy    
    pandas
    scipy
    sklearn



Required Data:
        `dream3.txt` -> a file containing Protein Protein Interactions
        `dream3_clusters.json`` -> a file containing clusters of proteins
        `dream3_go_results.tsv` -> file containing the GO terms corresponding to each protein in dream3

Files generated while running RECIPE:
        background_proteinlist 
        term mapping 
        querylists