scRNA-seq
Clustering_Options
Feature Plots
Compare with Sharma
Cluster Signatures
Choose a Cluster
Sub Feature Plots
Choose a Sub-cluster
ORA
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
6
7
8
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
Show/hide CellTypist
Choose Signature Sources
Top N
ORA Scope
Cluster vs. All
Sub-cluster vs. All
Sub-cluster vs. In-cluster
Which Cluster
Which Sub-cluster
ORA Type
GO
Kegg
Reactome
Other
Custom gene lists
CellMarkerDB
ClusterMole
McParland 2018 Liver w/Macrophages
MSigDB Hallmarks (the Broad)
Wu 2019 Spatial HCC Markers
Sharma Top 25
Filter for:
LogFC > 2 (above any turquoise line)
LogFC > Knee (left of blue line)
All Differentially Expressed
Top 25 (per Sharma top 25)
Run (or refresh)