How do I science?

Welcome to the Palomero Lab How-To guide! This guide covers a range of topics including:

  • Running bioinformatics tools and pipelines
  • Managing data with command-line interfaces
  • Writing effective scripts for automation
  • Setting up and using AWS services for high-performance computing
  • Using Rstudio and Jupyter notebooks for data analysis

Read more about this guide or visit the project's original GitHub repository.

Note

Lab members click here to access the private section of the guide.

How to use this guide

Browse the navigation bar, use the search function, or click through the pages to find the information you need.

Shell commands and code snippets will be formatted like this when written inline or in a code block like the one below.

# Click the clipboard icon to copy me!
echo "Hello, world!"

Important

If you get this following error while using zsh:

$ zsh: command not found: #

Then you need to run the following command to tell zsh to ignore comments:

setopt interactivecomments

To make this change permanent, add the command to your .zshrc file by either editing it with a text editor or running the following command:

echo "setopt interactivecomments" >> ~/.zshrc

Contributing

This guide is open-source and welcomes contributions. If you have a suggestion, correction, or new content to add, you can click the "Edit this page" link at the top of each page

Happy computing!

Created by Ryan D. Najac for the Palomero Lab at the Institute for Cancer Genetics.
Page last updated on 2024-10-17.