Network Oriented Repurposing of Drugs (NORDic): network identification and master regulator detection
Project description
Network Oriented Repurposing of Drugs (NORDic) package
(c) Clémence Réda, 2022.
Due to the presence of copyrighted databases, the license for this code is Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).
Environment
Create the environment using script install_environment.sh.
Using the "refractory epilepsy" application
Import the initial states from Mirza et al., 2017 and the M30 genes from Delahaye-Duriez et al., 2016
conda activate NORDic_env
python3 download_Refractory_Epilepsy_Data.py
conda deactivate
Building a Boolean network
You need to register to the LINCS L1000 database and the DisGeNet database and write up the corresponding credentials and API keys to files
from NORDic.NORDic_NI.functions import network_identification
solution = network_identification(file_folder, taxon_id, path_to_genes, ...)
The final network solution is written to <file_folder>solution.bnet.
Detection of master regulators
Using the filename in .bnet "network_name", the size k of the set of master regulators and the set of initial states states
from NORDic.NORDic_PMR.functions import greedy
S, spreads = greedy(network_name, k, states, ...)
The result file is named application_regulators.csv.
Network analysis with Cytoscape
Network analyses are performed with Cytoscape 3.8.0. You need to download the module CytoCtrlAnalyser (version 1.0.0). Then run
from NORDic.NORDic_NI.functions import solution2cytoscape
solution2cytoscape(solution, file_folder+"solution_minimal_cytoscape")
which will create a style file (in .xml) and a network file readable by Cytoscape (in .sif).
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