Full: CCDL Single-Cell RNA-Seq Workshop, Virtual, November 1st-5th, 2021

September 28, 2021

The Data Lab will hold our next virtual workshop running from November 1-5, 2021!

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

Virtual Workshop Structure

The workshop will take place on November 1-5, 2021 from noon to 5pm eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with our staff available for consultation. On Friday, November 5th, we will cover any final questions and allow you to present the projects you have worked on to the other workshop participants. View a past workshop schedule here to see what you can expect!

During lectures, Data Lab 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, our 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 Data Lab 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 will introduce selected pipelines for single-cell RNA-seq analysis through hands-on exercises and brief discussions of the underlying methods. Topics covered will include quality control, normalization, clustering, and visualization.
  • 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., Seurat vs. Scater for single-cell RNA-seq data pre-processing).
  • 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 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 single-cell 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.

For full consideration, please apply by Monday, October 11th. Applicants will be notified of their acceptance after registration is closed and all applications have been reviewed. Accepted workshop participants will be asked to provide a $100 deposit to reserve their seat. Deposits will be fully refunded upon workshop attendance.

The Data Lab will hold our next virtual workshop running from November 1-5, 2021!

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

Virtual Workshop Structure

The workshop will take place on November 1-5, 2021 from noon to 5pm eastern. Each day consists of lectures and designated time for attendees to work on exercise materials and their own projects with our staff available for consultation. On Friday, November 5th, we will cover any final questions and allow you to present the projects you have worked on to the other workshop participants. View a past workshop schedule here to see what you can expect!

During lectures, Data Lab 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, our 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 Data Lab 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 will introduce selected pipelines for single-cell RNA-seq analysis through hands-on exercises and brief discussions of the underlying methods. Topics covered will include quality control, normalization, clustering, and visualization.
  • 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., Seurat vs. Scater for single-cell RNA-seq data pre-processing).
  • 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 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 single-cell 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.

For full consideration, please apply by Monday, October 11th. Applicants will be notified of their acceptance after registration is closed and all applications have been reviewed. 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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