Pseudobulk Analysis with Decoupler and edgeR

[dianichj]

🚀 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

• 🧬 Understand pseudobulk analysis principles.
• 🛠️ Generate pseudobulk expression matrices with Decoupler.
• 📈 Perform differential expression analysis with edgeR.

✨ Key Points

• 🔄 Pseudobulk bridges single-cell and bulk RNA-seq data.
• 🧮 Decoupler enables pseudobulk matrix generation.
• 🛡️ edgeR is robust for differential expression in pseudobulk data.

📋 Pending Items

• Finalize tutorial last steps and instructions.
• Add final plots and figures 🖼️.
• Revise explanations for parameters and key steps 🧐.
• Review formatting and style ✍️.

💡 Feel free to review and share your feedback—your input is much appreciated! 🙌

[shiltemann]

thanks @dianichj! Just taking this out of draft mode so that our build testing will run

[shiltemann]

Thanks a lot @dianichj! Just a couple of very minor techincal suggestions below, but looks great :)

[shiltemann]

Thanks @dianichj this looks great. Added a few very minor formatting tweaks, but good to go from a technical perspective 👍

[pavanvidem]

please add pbmc tutorial in requirements

[bgruening]

Muhaaaa, this is cool!