Pathway Enrichment Analysis plots: easy R tutorial
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- čas přidán 23. 08. 2024
- In this tutorial, I will explain how to create pretty plots to visualise your pathway enrichment analysis results.
This Part 2 of my R tutorial series on Pathway Enrichment Analysis.
Check out Part 1 for a step-by-step tutorial on performing PEA analysis with clusterProfiler():
• Pathway enrichment ana...
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 enrichplot() package.
Hope you like it!
Code explained:
biostatsquid.c...
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If you liked this video or found it useful, please let me know! Your comments and feedback are very much appreciated😊 If you have questions, don't hesitate to leave me a comment down below, I will answer as soon as I can:)
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Don’t forget to subscribe if you don’t want to miss another video from me! -------------------------------------------------------------------------------------------------------------------- Other interesting resources for pathway enrichment analysis:
clusterProfiler package: bioconductor.o...
clusterProfiler publication: www.sciencedir...
More on Pathway Enrichment Analysis: biostatsquid.c...
Dataset from: rdrr.io/github...
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Hi, yet another great tutorial. I enjoy your tips and tricks like the saving of multiple plots at once. You also briefly covered ggarrange() and I think it would be cool if you someday did a brief tutorial on publication tips and tricks (specifically for figures and also maybe a project framework flowchart type figure) that you have used or wish you would've known about sooner. I really like the pathway map too and would be really interested to see more on that and how to get a more concise map. Thanks and I will keep an eye out for your new uploads!
Hi! Thanks so much for your comment, your feedback inspired me to create a 'ggplot2 tricks & tips' video (at least part 1!). You can have a look here: czcams.com/video/RMjbSn4dtKw/video.html
Hope you like it!!
Thank you very much for your easy-to-follow tutorial! I think you forgot the put the code "enrichres
Hi! A big thanks for your comment and for pointing that out for me!! I just added the extra snippet to the webpage:)
@@biostatsquid You're very welcome and thank YOU too!
Hello thank you for the tutorial I have GSEA results and have no idea how to calculate and add the generatio and bgratio. I was wondering if you can explain a bit more about this part
Hi, thanks for the this great video, I only have genes list and I just want to cluster kegg pathways into similar pathways, how can we do that ?
Can you do a video for pathway enrichment analysis using pathfindR package in R
I have a small doubt, hope you can clarify. I began splitting my differentially expressed genes df as upregulated or downregulated into 2 new dfs using tibble and dpylr, and then I saw your video on creating sub-dfs .. but I am not able to follow that part fully. But I could create my bg gene with terms and get the cluterprofiler step running! I did this : loaded_data_GOBP
Nice video! I could not understand what # Substitute names so they are annotated nicely in the heatmap later
df$diffexpressed
Super cool video! Can you explain EnrichR in a different video?
Great suggestion!:) I have a few more videos coming up soon but will add it to the list;)