DoubletFinder: Detect doublets in single-cell RNA-Seq data in R | Detailed workflow tutorial

A detailed walk-through of steps to find doublets in single-cell RNA sequencing datasets using doublet prediction R package - DoubletFinder. I hope you liked the video. I look forward to your comments under the comments section!


1) Data:
https://www.10xgenomics.com/resources...

3) Link to code:
https://github.com/kpatel427/YouTubeT...

4) DoubletFinder github:
https://github.com/chris-mcginnis-ucs...

5) DoubletFinder paper:
https://www.cell.com/cell-systems/pdf...

Chapters:
0:00 Intro
0:20 What are doublets?
1:30 Types of doublets
1:52 DoubletFinder needs 3 parameters
2:22 How does DoubletFinder work?
4:10 Strategies for pK optimization (ground-truth and no ground-truth)
4:41 Expected number of doublets
5:19 Best practices
6:34 Read data in R
9:30 QC and Filtering
12:26 Standard pre-processing steps
14:37 pK optimization steps
18:39 Setting nExp parameter value
20:54 Running DoubletFinder
21:49 Visualize doublets (UMAP)

Show your support and encouragement by buying me a coffee:
https://www.buymeacoffee.com/bioinfor...

To get in touch:
Website: https://bioinformagician.org/
Github: https://github.com/kpatel427
Email: [email protected]

#bioinformagician #bioinformatics #doubletfinder #doublets #10xgenomics #seurat #R #genomics #beginners #tutorial #howto #omics #research #biology #rnaseq #ngs