The Childhood Cancer Data Lab (Data Lab) develops tools and training programs to empower childhood cancer researchers to utilize data to make more robust discoveries.
The Childhood Cancer Data Lab is an initiative of Alex’s Lemonade Stand Foundation.
2024 August Introduction to Bulk RNA-seq and Reproducible Research Practices
Dates: 2024-08-19 through 2024-08-22
Pre-workshop Prep
- Please review the Code of Conduct.
- If you are new to using R, we’ve assembled some resources for getting starting with R that can optionally help prepare you for the workshop.
Setup instructions
This will be a hands-on workshop, so to maximize our time, please arrive having installed and set up the software that we will be using. We will not have time to do all of the setup during the workshop and accomplish all of our goals for the workshop, so it’s important to take the time to do this before the workshop begins!
Please to set aside ~2 hours to perform all setup tasks:
- Please follow these instructions to install and set up Slack
- We use Slack to communicate with you before, during, and after the workshop.
- For roughly half of the workshop, you will work locally on your laptops. For this, you will need to install and setup several pieces of software, including R, RStudio, several R packages, GitKraken, and a suitable text editor. Please find instructions for your computer’s operating system at the appropriate link below:
- For the other half of the workshop, we will use our RStudio Server rather than having you work locally.
- Once you have been given your RStudio Server username and temporary password, follow these instructions to log in to our RStudio server and change your password.
- You will need to create a GitHub account if you do not already have one and configure the GitKraken application, installed in the step above.
- If you do not already use a password manager (for example, BitWarden or 1Password), we strongly recommend signing up and setting it up for general use.
- During this workshop, you will need to keep track of sensitive passwords, and using a robust password management system is the most secure way to do so.
Schedule
For more details on the schedule for each day, click here.
Workshop Structure
A description of our plans and goals for the workshop can be found on the Workshop Logistics page. Please also refer to the schedule for information about timing and links relevant to each day. An overview of the modules we will cover and associated links can be found on the Workshop Materials page.
For this workshop, you will both be using your computer as well as Instructors will interactively lead you through all materials, either locally on your computer or on RStudio Server, depending on the instruction day.
During consultation sessions, Data Lab staff will be available to answer questions and provide 1:1 assistance as you work through exercise notebooks we provide or work with your own transcriptomic data. As needed, we recommend you follow these guidelines for posting errors so you can maximize others’ abilities to help you resolve any errors you encounter.