groverkaushal / tcell_toggle_tetrahedron

A tool for processing and analyzing RNA-Seq data. This tool downloads and converts the raw count values to TPM-normalized matrices and performs Gene Set Enrichment Analysis (GSEA) to output various plots.

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.