scRNA-seq
Clustering_Options
Feature Plots
Compare with Sharma
Cluster Signatures
Choose a Cluster
Sub Feature Plots
Choose a Sub-cluster
Analyze cell type
Choose Clustering
Choose Feature
Gene, highly variable (HVG 3k)
Gene (non-HVG)
Plot as:
Expressed (yes/no)
Log(Normalized Value)
Show sub-clusters (columns) for:
Which Cluster
Top N Genes
10
10
Cell type notes:
Save note
Choose Signature Sources
Top N
Choose Feature
Gene, highly variable (HVG 3k)
Gene (non-HVG)
Plot as:
Expressed (yes/no)
Log(Normalized Value)
Which Sub-cluster
Top N Genes
10
10
Cell type notes:
Save note
Choose Signature Sources
Top N
Decision tree model (10-15 minutes run time when contrast is all clusters):
Contrast with clusters or subs
All
Specific
Control for effects of
#UMI
#Genes
%MT
#MT
patient
tumor/adj/normal
Segment based on
Database Signatures
Genes
Run
Contrast vs.
All other
Complexity parameter
0.005
0.005