Chapter 1 Introduction

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giovannellilab made-with-Markdown Maintenance

This book contains the code snippets and a wiki with all the codebases from the Giovannelli Lab. It is meant to be a growing repository of organized recipes for solving code issues we have encountered over the years. The wiki also provides links to full-on tutorials containing our juicier pipelines. Feel free to correct errors, suggest changes and different solutions and add to our codebase using issues and pull requests.

1.1 Design principles

The wiki is organized in sections based on the …well, I’m still thinking about it. Standalone scripts are in the scripts folder and can be used directly for their intended purpose. A brief description is present on the wiki. Small functions and one-liners (or few liners) can be copied and pasted directly in Jupyter or RStudio (or the terminal for that matter).

1.2 Credits

We tried to cite all the sources where we found the solutions we are implementing. If you see something that we did not credit appropriately please let us know. If you decide to use some of the scripts here, fantastic! If you wanna let us know that you are using them, drop us a line on social media or via email. If for whatever reasons you wanna cite this codebase, please use:

Giovannelli, D and the Giovanelli Lab members. 2023. Solving common bioinformatic problems across large collaborative projects: creating a shared codebase on GitHub. doi: to be assigned

Thank you and have fun!