The Quayle Lab is dedicated to cutting-edge research in cancer bioinformatics, with a focus on leveraging computational methods to understand and combat cancer. This organisation serves as a centralised hub for all research projects conducted by members of the lab, including PhD students, postdoctoral researchers, and collaborators.

Our lab combines expertise in high-throughput multi-omics techniologies, bioinformatics, data science, and machine learning to analyse and interpret large-scale cancer datasets. We are committed to contributing to the scientific community through open-source research, code, and collaborative projects that aim to unravel the complexities of cancer biology.

The main goals of this GitHub organisation are:

• Centralising Research: Provide a common platform for all lab members to share and manage their research code.
• Collaboration: Encourage collaboration among lab members, as well as with external collaborators and the broader scientific community.
• Transparency & Reproducibility: Promote transparent, reproducible research by sharing code and documentation in an open-access format.

Each repository within this organisation represents a distinct project within the Quayle Lab. For example:

• project-name-phd-student: Project repositories for PhD students
• common-tools: Repositories for shared tools, scripts, or pipelines used by the lab
• collaborative-projects: Joint projects with other labs or research groups

If you are a member of the Quayle Lab, please adhere to the following guidelines when working within this GitHub organisation:

• Each project should have its own repository. Use a consistent naming format: date(ISO8601)_project_title_studentname (e.g., 2023_12_30_tumour_genomics_janedoe).
• Include a README file in your repository that provides an overivew of:
  • Project background
  • Objectives
  • Methodology
  • How to use/replicate your analyses
  • Contact details

• Use meaningful commit messages that describe changes made.
• Work within branches when developing new features or analyses, and merge back into main only after thorough testing.

• Provide clear, detailed documentation for your code, including comments, usage instructions, and any necessary dependencies.
• Use RMarkdown, Jupyter Notebooks, or similar tools to create reproducible workflows when possible.
• Store data responsibly, ensuring that sensitive or large datasets are not included in the repository. Instead, provide instructions on how to access or download them.

• Collaborate with other members by reviewing pull requests, providing feedback, and sharing ideas.
• Use GitHub Issues to track bugs, suggest enhancements, or discuss aspects of your project.

For any questions about this organisation or if you need access, please contact Dr Lewis A Quayle at [email protected].

We encourage collaboration, so feel free to reach out if you'd like to contribute or have an idea for a new project!

Thank you to all the members of the Quayle Lab for your dedication to advancing cancer bioinformatics research. Together, we can make significant strides in understanding and treating cancer.