Metagenomics Project: Relative Enzyme Abundance

This repository contains the analysis and code used to determine the relative abundance of specific enzymes within a metagenomic dataset.

How to Run the Analysis

Prerequisites

To run the analysis locally, you will need the following software and Python libraries:

• Python 3.x
• Jupyter Notebook
• pandas
• numpy
• matplotlib or seaborn

Installation

1. Clone the repository:

   git clone [https://github.com/zeyneperten/metagenomics.git](https://github.com/zeyneperten/metagenomics.git)
   cd metagenomics

2. Install dependencies (if using a requirements file):

   # If you have a file named requirements.txt
   pip install -r requirements.txt

   (Or list the libraries individually if you don't have a requirements file.)
3. Launch the notebook:

   jupyter notebook relative_abund_enzyme.ipynb
   

Datasets used while writing the code:

Fan KC et al., "Compositional and functional gut microbiota alterations in mild cognitive impairment: links to Alzheimer's disease pathology.", Alzheimers Res Ther, 2025 May 30;17(1):122

Laske C, Müller S, Preische O, et al. Signature of Alzheimer's Disease in Intestinal Microbiome: Results From the AlzBiom Study. Front Neurosci. 2022;16:792996. Published 2022 Apr 19. doi:10.3389/fnins.2022.792996

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Author: [Zeynep Erten]