This repository contains an interactive Streamlit app for processing and visualizing GEO data from NCBI's Gene Expression Omnibus. The web app allows users to derive datasets from GEO and automatically perform data preprocessing such as normalization, filtering, and differential expression. This app can be useful for researchers who are working with RNA-Seq data and trying to identify differentially expressed genes for further analysis.
- Parsing of GEO formatted files
- Auto data cleansing and processing
- Quality control including PCA and heatmap analysis
- Differential expression analyses based on predefined criteria, with visualization and figure download options
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To run the app locally, first clone the repository:
git clone https://github.com/mitumh3/GEO-dataprocess-streamlit.gitNext, navigate to the directory and install the necessary packages. It's recommended to use a virtual environment to install the packages.
pip install -r requirements.txtTo run the app, type:
streamlit run scripts/src/main.py