Full: Data Lab Bulk RNA-Seq and Reproducible Research Practices Workshop, Minneapolis, August 19-22, 2024

July 16, 2024

We are excited to announce that our next workshop, Introduction to Bulk RNA-Sequencing and Reproducible Research Practices, will take place in Minneapolis, MN from August 19-22, 2024! In this workshop, Data Lab staff will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, bulk RNA-seq data analysis, pathway analyses, and techniques to achieve reproducible results in computational cancer research.

About the workshop

The workshop will take place on August 19-22 from 9am-5pm at the University of Minnesota. 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 the final day of the course, we will cover any final questions and participants will present the projects they have worked on to the group.

Participants should plan to bring their own laptop. We will provide breakfast, lunch, beverages, and snacks! Attendees will also be invited to join us for a group dinner.

Travel reimbursement up to $500 is available for qualifying participants who reside over 50 miles from the workshop location. To qualify for reimbursement, attendees must note this request on their application, be able to provide documentation of their travel expenses, and attend the entirety of the workshop.

What you will learn

  • We will introduce you to the R programming language and R Notebooks
  • We cover selected pipelines for quality control, processing raw sequence data to obtain 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

We will also cover some common practices for reproducible research, including:

  • Organizing your projects, including data, code, and documentation
  • Navigating your computer from the command line interface
  • Tracking and automating your work with scripts
  • Making your code more readable, robust, and reusable - by you and by others!
  • Maintaining and tracking changes in your projects and code over time with Git and GitHub
  • Managing and tracking software and package versions for improved reproducibility

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. We will share 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 for your own work, particularly for complex experimental designs
  • We won't cover all the features and foibles of Git and GitHub
  • We won't cover workflow management systems such as CWL, Snakemake, or Nextflow

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 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.

Please feel free to reach out to us at training@ccdatalab.org with any questions. Applications will close when all spots are full and no later than July 26, whichever comes first. Applicants will be notified of their status 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 excited to announce that our next workshop, Introduction to Bulk RNA-Sequencing and Reproducible Research Practices, will take place in Minneapolis, MN from August 19-22, 2024! In this workshop, Data Lab staff will introduce researchers studying pediatric cancer to the R programming language, the Tidyverse R packages for data science, bulk RNA-seq data analysis, pathway analyses, and techniques to achieve reproducible results in computational cancer research.

About the workshop

The workshop will take place on August 19-22 from 9am-5pm at the University of Minnesota. 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 the final day of the course, we will cover any final questions and participants will present the projects they have worked on to the group.

Participants should plan to bring their own laptop. We will provide breakfast, lunch, beverages, and snacks! Attendees will also be invited to join us for a group dinner.

Travel reimbursement up to $500 is available for qualifying participants who reside over 50 miles from the workshop location. To qualify for reimbursement, attendees must note this request on their application, be able to provide documentation of their travel expenses, and attend the entirety of the workshop.

What you will learn

  • We will introduce you to the R programming language and R Notebooks
  • We cover selected pipelines for quality control, processing raw sequence data to obtain 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

We will also cover some common practices for reproducible research, including:

  • Organizing your projects, including data, code, and documentation
  • Navigating your computer from the command line interface
  • Tracking and automating your work with scripts
  • Making your code more readable, robust, and reusable - by you and by others!
  • Maintaining and tracking changes in your projects and code over time with Git and GitHub
  • Managing and tracking software and package versions for improved reproducibility

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. We will share 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 for your own work, particularly for complex experimental designs
  • We won't cover all the features and foibles of Git and GitHub
  • We won't cover workflow management systems such as CWL, Snakemake, or Nextflow

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 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.

Please feel free to reach out to us at training@ccdatalab.org with any questions. Applications will close when all spots are full and no later than July 26, whichever comes first. Applicants will be notified of their status 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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