This project takes a GSEID as input and downloads the GSE dataset and its annotation table. It then implements certain algorithms to generate 76GS score, KS Score, and MLR Score for each GSM ID. Then it generates a plot of which correlates the scores obtained from the 3 methods.
Make sure you have matlab runtime R2023a installed on your device. It can be installed from:-
https://in.mathworks.com/products/compiler/matlab-runtime.html
Clone the repsitory
git clone https://github.com/Blassreiter0/EMT_score_python_implementation.git
Create a virtual environment:
python -m venv venv
Activate the virtual environment:
source venv/bin/activate
Install the requirements:
pip install -r requirements.txt
go inside the repository using the command: cd .\EMT_score_python_implementation\
Open the main.py file from any IDE. Run it and Then enter any GSEID(for Eg. GSE21422).
This code is the python implementation of work from github projects:-
https://github.com/priyanka8993/EMT_score_calculation
https://github.com/sushimndl/EMT_Scoring_RNASeq
for more information:
Chakraborty P, George JT, Tripathi S, Levine H and Jolly MK (2020) Comparative Study of Transcriptomics-Based Scoring Metrics for the Epithelial-Hybrid-Mesenchymal Spectrum. Front. Bioeng. Biotechnol. 8:220. doi: 10.3389/fbioe.2020.00220