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Overview

Below is an overall description of our tool. For details and citations about this work, please check:

System Requirements

  • Python 3.11.4

Installation

  1. Create a virtual environment:

    python 3.12.1 -m venv venv_name

  2. Activate the virtual environment:

    source venv/bin/activate

  3. Install required packages:

    pip install -r requirements.txt

Usage

Step 1: Download Raw Count Values

Run gseconverter.py by providing the GSE id as input:

input_gseid = "GSE210222"

This code will download soft and gpl files and create a tab-separated .csv file with raw count values.

Step 2: Convert to TPM

Execute tpm_converter.py to convert the counts matrix file to a TPM-normalized matrix.

Step 3: GSEA Analysis

Run ssgsea.py by providing the matrix.csv file and genesets.gmt file for GSEA analysis. The code will generate a scatter plot of samples with PCA values.

Step 4: Generate Plots

Finally, execute main.py to generate plots showcased in the paper.

Important Note

For RNA-Seq data where the .soft file lacks matrix values, download the matrix file separately.

License

This project is licensed under the MIT License.