scRNA-seq
Clustering_Options
Feature Plots
Compare with Sharma
Cluster Signatures
Choose a Cluster
Cluster gene signature
Sub Feature Plots
Choose a Sub-cluster
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
Load saved signature
Keyword for signature name
Save
Test new signature:
Differential expression type
Positive only
Positive and negative
Control for effects of
#UMI
#Genes
%MT
#MT
Assay
SCT
RNA
RNA scale
Use logarithms
#UMI
#Genes
%MT
#MT
Gene expr (not if SCT)
Method
Logistic Regression
Decision Tree
Run
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