SSG

Table of Contents

• Installation
• Usage
• Features

Installation

poetry install

Prerequisites

• python>=3.11
• poetry>=1.8.3

Steps

1. Clone the repository:

   git clone https://github.com/BioTechCo/SSG.git

2. Navigate to the project directory:

   cd SSG

3. Install dependencies:

    poetry install

Usage

1. geo_champ.ipynb: This notebook fetches data from GEO database via FTP server and GEOparse. The critical phenotypes are identified and a sample sheet suitable for ChAMP analysis is generated.

Warning

The one phenotype differentiating tumor and normal samples is identified by selecting the phenotype with exactly two unique values. Users might need to manually select the phenotype of interest if more than one phenotype has two unique values.

2. champ_analysis.ipynb: This notebook fetch Data tables by specific GEO accession. Users are encouraged to visit the GEO database and look up whether the data is normalized, which is often presented in Data table header descriptions of every sample.

3. geo_phenotype.ipynb: This notebook fetch phenotypes form GEO database and export them as a csv file. Excluded phenotypes are those names containing supplementary_file, data_processing, extract_protocol_ch1, hyb_protocol, contact.

Features

• Generate sample sheet for ChAMP analysis by specific GEO accession.
• Fetch data tables by specific GEO accession.
• Fetch phenotypes by specific GEO accession.