Find markers and cluster identification in single-cell RNA-Seq using Seurat | Workflow tutorial

A detailed walk-through of steps to find canonical markers (markers conserved across conditions) and find differentially expressed markers in a particular cell type between conditions using Seurat's find markers functions in R. I hope you find the video informative. I look forward to your comments under the comments section!

1) Data:
https://drive.google.com/file/d/13I22...

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

3) Vignettes:
▸ https://satijalab.org/seurat/articles...
▸ https://satijalab.org/seurat/articles...
▸ https://hbctraining.github.io/In-dept...

4) Marker databases:
1. SCSig: http://www.gsea-msigdb.org/gsea/msigd...
2. PangloDB: https://panglaodb.se/
3. CellMarker: http://bio-bigdata.hrbmu.edu.cn/CellM...


Chapters:
0:00 Intro
0:36 findMarkers(), findAllMarkers(), findConservedMarkers()
4:09 Study design
4:57 Load data
6:20 Visualize by clusters and condition
9:15 findAllMarkers()
12:51 DefaultAssay 'RNA'
14:10 findConservedMarkers() for cluster 3
17:12 Visualize canonical markers in a FeaturePlot
20:15 RenameIdents
21:55 Annotating clusters and marker databases
23:56 Annotating rest of the clusters
26:21 Perform differential expression in CD16 Monocytes between conditions (findMarkers())
30:52 Visualize markers identified by findConservedMarkers() vs findMarkers()

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 #findmarkers #findallmarkers #findconservedmarkers #deg #seurat #integration #cca #R #genomics #beginners #tutorial #howto #omics #research #biology #ncbi #GEO #rnaseq #ngs