Pseudobulk Analysis with Decoupler and edgeR #5617
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added single-cell tag: "tags": ["single-cell"]
Edited Tags in Workflow file
Added edgeR explanation for performing DE in pseudobulk aggregates.
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The failing test is because of:
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Thanks a lot @dianichj! This looks good, just a couple broken boxes and formatting tweaks (see below)
Just out of curiosity, are you all set up to get a local preview of your tutorial? This can also be done online using CodeSpaces now (see tutotrial)
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| In this tutorial, we will guide you through a pseudobulk analysis workflow using the **Decoupler** and **edgeR** tools available in Galaxy ({% cite Badia-iMompel2022 %}) ({% cite Liu2015 %}). These tools facilitate functional and differential expression analysis, and their output can be integrated with other Galaxy tools to visualize results, such as creating Volcano Plots, which we will also cover in this tutorial. | ||
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| > <agenda-title>Pseudobulk Analysis Pipeline Agenda</agenda-title> |
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the agenda will be automatically generated based on your section titles, pleas replace this with
> <agenda-title></agenda-title>
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> In this tutorial, we will cover:
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> 1. TOC
> {:toc}
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{: .agenda}
| > 1. What are the output(s) of the edgeR tool? | ||
| > 2. How can we interpret our output result file? | ||
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| > <solution-title>edgeR Outputs and Interpretation</solution-title> |
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since these boxes are nested, make sure to add a > in front of this line and every line below until the end of the solution box
| # Key Takeaways and Recommendations | ||
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| ## Key Takeaways | ||
| - **Pseudobulk Analysis Advantage:** Pseudobulk analysis bridges single-cell and bulk RNA-seq approaches, combining high resolution with statistical robustness. |
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anything you add in key_points metadata will be added in a box at the end of the tutorial, so you could consider moving these there.
Thanks a lot for all your comments, Saskia! I will check it again locally after going over all your revisions and will ping you with a comment. 😊 |
Co-authored-by: Saskia Hiltemann <[email protected]>
Co-authored-by: Saskia Hiltemann <[email protected]>
Co-authored-by: Saskia Hiltemann <[email protected]>
Co-authored-by: Saskia Hiltemann <[email protected]>
Co-authored-by: Saskia Hiltemann <[email protected]>
I did not know this Saskia. Thanks for mentioning it! I was following this. I noticed the linked you mentioned here is available here but I think the link in the README is the one that a new user would check. Thanks. |
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@dadrasarmin that is a very good point, I tend to forget about the README file, I will update that! |
🚀 Pseudobulk Analysis with Decoupler and edgeR
Summary
This tutorial introduces pseudobulk analysis using Decoupler and edgeR in Galaxy 🌌. It covers data preparation, generating pseudobulk expression matrices, and performing differential expression analysis, including a Volcano Plot for final visualization of results 🌋📊.
🔗 Zenodo Link
https://zenodo.org/records/13929549
🎯 Objectives
✨ Key Points
📋 Pending Items
💡 Feel free to review and share your feedback—your input is much appreciated! 🙌