Full: CCDL RNA-Seq Workshop, Virtual, March 22nd - 26th, 2021

February 15, 2021

We are delighted to announce a virtual workshop running from March 22 - 26, 2021!

In this workshop, CCDL staff will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, bulk RNA-seq data analysis, and pathway analyses.

Virtual workshop structure

The workshop will take place on March 22 - 26, 2021 from noon - 5pm Eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with CCDL staff available for consultation. On Friday, March 26th, we will cover any final questions and allow you to present the projects you have worked on to the other workshop participants. See a draft of our workshop schedule here!

During lectures, CCDL staff will lead you through course material using Zoom, Slack, and RStudio Server. We will record instruction and provide it to workshop attendees so they can revisit it outside of workshop hours or in case they experience disruptions during live instruction.

During consultation time, CCDL staff will be available to answer questions and provide any 1:1 assistance as you work through exercise notebooks we provide or work with your own transcriptomic data. We’ll use Zoom and Slack for this, too.

You’ll need a laptop with internet access and to install Zoom & Slack. You will log into an RStudio Server hosted by the CCDL from your web browser.

What you will learn

  • We will introduce you to the R programming language, R Notebooks, and some reproducible research practices.
  • We cover selected pipelines for quality control, processing to gene expression estimates, and basic downstream analysis of bulk RNA-seq data through hands-on exercises with brief discussions of the underlying methods.
  • We  will introduce common approaches for pathway analysis.
  • Our workshop’s curriculum is generally designed to go broad and not deep.

We do not assume prior programming experience, but the course will move quickly and we have assembled some resources for learning R basics to help make the most of our time together.

What you won’t learn

  • We don’t address experimental design (e.g., how many replicates you need).
  • We won’t compare tools (e.g., edgeR vs. DESeq2 for differential gene expression).
  • We won’t cover every feature or assumption of the tools we do present, but we will try to highlight the features and gotchas that we think are relevant to most users.
  • You may not be able to perform every analysis you need to perform for your own work, particularly for complex experimental designs.

Apply now!

If you are a pediatric cancer researcher and this sounds like it’s for you, please apply now!

To ensure that workshop attendees have a great hands-on experience, there will be a very limited number of seats available. We will prioritize applicants that have bulk transcriptomic data that they are currently using to answer questions in pediatric cancer research. If you are a pediatric cancer research with an interest in analyzing scRNA-seq data, we will announce a workshop focused on scRNA-seq at a later date. Please feel free to reach out to us at training@ccdatalab.org with any questions.


For full consideration, please apply by Monday, March 1st. Applicants will be notified of their acceptance on a rolling basis. Accepted workshop participants will be asked to provide a $100 deposit to reserve their seat. Deposits will be fully refunded upon workshop attendance.


We are delighted to announce a virtual workshop running from March 22 - 26, 2021!

In this workshop, CCDL staff will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, bulk RNA-seq data analysis, and pathway analyses.

Virtual workshop structure

The workshop will take place on March 22 - 26, 2021 from noon - 5pm Eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with CCDL staff available for consultation. On Friday, March 26th, we will cover any final questions and allow you to present the projects you have worked on to the other workshop participants. See a draft of our workshop schedule here!

During lectures, CCDL staff will lead you through course material using Zoom, Slack, and RStudio Server. We will record instruction and provide it to workshop attendees so they can revisit it outside of workshop hours or in case they experience disruptions during live instruction.

During consultation time, CCDL staff will be available to answer questions and provide any 1:1 assistance as you work through exercise notebooks we provide or work with your own transcriptomic data. We’ll use Zoom and Slack for this, too.

You’ll need a laptop with internet access and to install Zoom & Slack. You will log into an RStudio Server hosted by the CCDL from your web browser.

What you will learn

  • We will introduce you to the R programming language, R Notebooks, and some reproducible research practices.
  • We cover selected pipelines for quality control, processing to gene expression estimates, and basic downstream analysis of bulk RNA-seq data through hands-on exercises with brief discussions of the underlying methods.
  • We  will introduce common approaches for pathway analysis.
  • Our workshop’s curriculum is generally designed to go broad and not deep.

We do not assume prior programming experience, but the course will move quickly and we have assembled some resources for learning R basics to help make the most of our time together.

What you won’t learn

  • We don’t address experimental design (e.g., how many replicates you need).
  • We won’t compare tools (e.g., edgeR vs. DESeq2 for differential gene expression).
  • We won’t cover every feature or assumption of the tools we do present, but we will try to highlight the features and gotchas that we think are relevant to most users.
  • You may not be able to perform every analysis you need to perform for your own work, particularly for complex experimental designs.

Apply now!

If you are a pediatric cancer researcher and this sounds like it’s for you, please apply now!

To ensure that workshop attendees have a great hands-on experience, there will be a very limited number of seats available. We will prioritize applicants that have bulk transcriptomic data that they are currently using to answer questions in pediatric cancer research. If you are a pediatric cancer research with an interest in analyzing scRNA-seq data, we will announce a workshop focused on scRNA-seq at a later date. Please feel free to reach out to us at training@ccdatalab.org with any questions.


For full consideration, please apply by Monday, March 1st. Applicants will be notified of their acceptance on a rolling basis. Accepted workshop participants will be asked to provide a $100 deposit to reserve their seat. Deposits will be fully refunded upon workshop attendance.


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