Full: CCDL RNA-Seq Workshop, Virtual Pilot, May 4-8th, 2020

April 20, 2020

Note: We have received a large volume of applications and are no longer accepting applications to this pilot workshop.

We at the Childhood Cancer Data Lab are as committed as ever to our mission of empowering pediatric cancer experts poised for the next big discovery with the knowledge, data, and tools to reach it.

Last year, the CCDL ran four in-person workshops in four US cities and planned to hold as many this year. Like many of the researchers we serve, our plans are on hold.

We know that pandemic-related university closures mean that the demand for opportunities for pediatric cancer researchers to increase their analytical skills has never been higher. As such, we are delighted to announce a pilot virtual workshop running from May 4-8, 2020!

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

Virtual workshop structure

The workshop will take place on May 4-8, 2020 from noon-4pm Eastern and be divided into instruction days (Monday, May 4th and Wednesday, May 6th) and consultation days (Tuesday, May 5th and Thursday, May 7th). On Friday May 8th, we will reconvene to cover any final questions and to allow you to present the projects you have worked on to the other workshop participants. You can take a look at the tentative virtual schedule here.

On instruction days, 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. (Don’t worry, we don’t understand the passage of time anymore, either!)

On consultation days, 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 these days, too.

What you will need

You’ll need a computer with internet access and to install Zoom & Slack (Windows instructions, Mac instructions, Linux instructions coming soon). You will log into an RStudio Server hosted by the CCDL from your web browser.

What you will learn

  • 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.
  • Our workshop’s curriculum is generally designed to go broad and not deep.

We assume no prior programming experience, but 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.

We are no longer accepting applications

We have received a large volume of applications and are no longer accepting applications to this pilot workshop. Click the link below to sign up to be notified when future workshops are announced.

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 transcriptomic data that they are currently using to answer questions in pediatric cancer research. Please feel free to reach out to us at training@ccdatalab.org with any questions.

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.

Note: We have received a large volume of applications and are no longer accepting applications to this pilot workshop.

We at the Childhood Cancer Data Lab are as committed as ever to our mission of empowering pediatric cancer experts poised for the next big discovery with the knowledge, data, and tools to reach it.

Last year, the CCDL ran four in-person workshops in four US cities and planned to hold as many this year. Like many of the researchers we serve, our plans are on hold.

We know that pandemic-related university closures mean that the demand for opportunities for pediatric cancer researchers to increase their analytical skills has never been higher. As such, we are delighted to announce a pilot virtual workshop running from May 4-8, 2020!

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

Virtual workshop structure

The workshop will take place on May 4-8, 2020 from noon-4pm Eastern and be divided into instruction days (Monday, May 4th and Wednesday, May 6th) and consultation days (Tuesday, May 5th and Thursday, May 7th). On Friday May 8th, we will reconvene to cover any final questions and to allow you to present the projects you have worked on to the other workshop participants. You can take a look at the tentative virtual schedule here.

On instruction days, 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. (Don’t worry, we don’t understand the passage of time anymore, either!)

On consultation days, 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 these days, too.

What you will need

You’ll need a computer with internet access and to install Zoom & Slack (Windows instructions, Mac instructions, Linux instructions coming soon). You will log into an RStudio Server hosted by the CCDL from your web browser.

What you will learn

  • 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.
  • Our workshop’s curriculum is generally designed to go broad and not deep.

We assume no prior programming experience, but 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.

We are no longer accepting applications

We have received a large volume of applications and are no longer accepting applications to this pilot workshop. Click the link below to sign up to be notified when future workshops are announced.

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 transcriptomic data that they are currently using to answer questions in pediatric cancer research. Please feel free to reach out to us at training@ccdatalab.org with any questions.

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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