A README template

This is an example of what a README file should include: a brief overview of the project, installation instructions, usage examples, details on dependencies, and any other relevant information to help others understand and reproduce your work.

1. Overview

A brief summary of the project, its purpose, and the biological questions it aims to address.

2. Requirements

List of any software, packages, or tools needed to run the analysis, e.g., R version, specific R packages and versions, command line tools.

3. Installation

Instructions on how to set up the environment and install any necessary dependencies. If using renv, include steps for restoring the environment, for example:

# Install renv, if needed 
install.packages("renv")

# Restore the environment
renv::restore()

4. Data

Explanation of the raw and processed data used in the project, where it comes from, and any important notes about it (e.g., data format, sources). Give enough detail so that someone could reproduce the results (in principle).

5. Scripts

A brief overview of the main scripts in the project and what each one does.

Example:

01_import_data.R: Loads raw data into the workspace.

02_clean_data.R: Processes and cleans the raw data.

03_analyse_data.R: Performs the main data analysis.

04_plot_results.R: Creates visualisations based on the analysis.
6. Running the Analysis

Step-by-step instructions on how to execute the analysis, typically referencing the scripts in the correct order.

7. Outputs

Description of the output files generated by the project (e.g., figures, tables) and where they are saved.


8. References/Future Work

List any papers, books, or resources used in the project, including methods or data sources.

Brief section on any planned improvements, additional analyses, or next steps for the project.