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
1
2
3
4
5
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9
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
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
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
1e-04
5e-04
0.001
0.005
0.01
0.05
0.1