Incubator Lesson Spotlight: Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor

The Incubator Lesson Spotlight highlights a lesson under development by our community in The Carpentries Incubator. In this edition, we look at the progress being made on the Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor lesson, and hear from the authors about how The Carpentries community can get involved with the ongoing development of this lesson.

Lesson Profile

• Title: Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
• Lesson Pages: https://carpentries-incubator.github.io/bioc-rnaseq
• Lesson Repository: https://github.com/carpentries-incubator/bioc-rnaseq

Learning Objectives

After following this lesson, learners will be able to:

• choose an appropriate design for a bulk RNA Sequencing experiment.
• import and annotate quantified RNA-Seq data in R.
• assess the quality of experimental results represented as a gene expression matrix.
• run a standard differential expression analysis and interpret the output.
• execute a gene set analysis.

Target Audience

This lesson is aimed at researchers who are already aware of what Bioconductor is and how it can benefit their data analysis. They are comfortable with basic operations in R, such as creating numeric, character vector, and data frame variables, installing and loading packages from CRAN and Bioconductor, and visualising data in common formats such as bar and scatter plots. These researchers want to learn how to use R and Bioconductor to explore and analyse data produced in bulk RNA sequencing experiments, and visualise and interpret the results of these analyses.

Lesson Progress

The Bioconductor Training Group has been meeting monthly, with the aim of developing several lessons in The Carpentries Incubator. We are in the early stages of creating content based on an outline for the Analysis and Interpretation of Bulk RNA-Seq Data lesson. (The other two lessons under development are introductory lessons to Bioconductor and Bioconductor Projects.) On August 5, we will host a dedicated lesson development workshop at BioC2021 with the goal of making further progress.

How You Can Help Develop This Lesson

We would welcome other members of The Carpentries and Bioconductor communities who wish to contribute to the development of this lesson, by joining us in designing and writing lesson content, testing it in their workshops, and providing feedback as the lesson grows.

If you would like to get involved in this project, please join the Bioconductor Teaching Google Group and send a message to the group and/or attend one of our monthly meetings where we discuss and develop the lessons. You might also consider registering to attend the workshop session at the Bioc2021 conference.

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About This Series

Incubator Lesson Spotlight is a regular feature in The Carpentries blog and Carpentries Clippings newsletter, highlighting the great work our community is doing to develop new lessons in The Carpentries Incubator. Developers of any lesson in the Incubator are encouraged to submit details about their material for inclusion in the series. If you would like to increase the visibility of your lesson and encourage Carpentries community members to contribute to its ongoing development, fill in this short form.