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:
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2) Link to code:
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3) Vignettes:
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4) Marker databases:
1. SCSig: [ Ссылка ]
2. PangloDB: [ Ссылка ]
3. CellMarker: [ Ссылка ]
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:
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To get in touch:
Website: [ Ссылка ]
Github: [ Ссылка ]
Email: khushbu_p@hotmail.com
#bioinformagician #bioinformatics #findmarkers #findallmarkers #findconservedmarkers #deg #seurat #integration #cca #R #genomics #beginners #tutorial #howto #omics #research #biology #ncbi #GEO #rnaseq #ngs
