Basic Utility Script for Bacteria and Host-Microbe Interactions Analysis

This repository contains a basic utility script that can be used for analyzing bacteria and host-microbe interactions using omics data. It provides a set of functionalities that are commonly used in bioinformatics and can be a useful starting point for researchers working in this field.

Features

• Bioinformatic processing: The script includes functions for preprocessing omics data, such as quality control, filtering, normalization, and transformation.

• Statistical analysis: It offers various statistical analysis methods for identifying differentially expressed genes, proteins, or metabolites between different conditions or groups.

• Visualization: The script includes functions for generating visualizations, such as heatmaps, volcano plots, and pathway enrichment plots, to aid in data exploration and interpretation.

• Documentation: The script is thoroughly documented, providing explanations and examples for each function to facilitate its usage and customization.

Requirements

The script requires the following dependencies to be installed:

• Python (version 3.10)
• R (version 4.2)
• Bioconductor packages (e.g., limma, edgeR)
• Other Python libraries (e.g., pandas, numpy, matplotlib)

But all requirements can easily be installed with conda, like:

git clone https://github.com/JacobAgerbo/Basic_Utils.git 
cd Basic_Utils
conda env create -f Basic_Utils.yml
conda activate Basic_Utils

Now you are ready to go!

Usage

To use the script, follow these steps:

1. Clone the repository to your local machine.
2. A basic conda environment called Basic_Utils will be the foundation of these bioinformatic processes.
3. Now you should be able to run all the scripts in this repository.

Contributions

Contributions to this utility script are welcome. If you have any suggestions or improvements, feel free to open an issue on the repository.

License

This project is licensed under the MIT License.

Contact

For any questions or inquiries, please contact jacob.rasmussen@bio.ku.dk.

Note: This utility script is provided as-is and may require customization based on your specific research needs. It is recommended to thoroughly review and modify the script according to your requirements before using it in a production environment.