In this tutorial, I will explain how to perform pathway enrichment analysis on your differential gene expression analysis results. We will use the R package clusterProfiler() and you will learn how to:
- Download and use gene sets in the context of PEA
- Prepare your differential gene expression results for PEA
- Perform functional enrichment analysis with clusterProfiler()
- and interpret the results!
In part 2, we will explore various plots to visualise your results!
https://youtu.be/TWiN_qNmYX0
And as always, you can find the code I am using in this tutorial at biostatsquid.com, where you can also find a step by step explanation of the code. For this tutorial you will need R, or Rstudio, and you will need to install the clusterProfiler() package.
Hope you like it!
Code explained: https://biostatsquid.com/pathway-enrichment-analysis-tutorial-clusterprofiler/
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Other interesting resources for pathway enrichment analysis:
clusterProfiler package: https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
clusterProfiler publication: https://www.sciencedirect.com/science/article/pii/S2666675821000667
More on Pathway Enrichment Analysis: https://biostatsquid.com/pathway-enrichment-analysis-explained/
Dataset from: https://rdrr.io/github/LTLA/scRNAseq/man/BacherTCellData.html
Music from #Uppbeat (free for Creators!):
https://uppbeat.io/t/pecan-pie/east-side-horns
License code: 80ZOLNQ8NSDSWKFV