CytoTalk App
Under development
© CytoTalk LLC 2020
Read Data
Handling metadata
Abundance Visualization
Data Preprocessing
Cell Type Annotation
Gene Set Scoring
Image Viewer
Feature Stats
scRNA-seq visualize
DEGs
CellChat Analysis
Annotate CSV File
Upload Seurat Object (.rds)
Browse...
Manage Objects
Select Object to Set Active:
Set Active
Select Default Assay:
Set as Default
Select Object to Edit Note:
Note for selected object:
Save Note
Select Object to Remove:
Remove Selected Object
Upload 10X Files
Matrix File (matrix.mtx.gz)
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Features File (features.tsv.gz)
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Barcodes File (barcodes.tsv.gz)
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Read10X Parameters
gene.column
cell.column
unique.features
strip.suffix
CreateSeuratObject Parameters
min.cells
min.features
Project Name
Assay
names.field
names.delim
Upload Metadata (CSV, optional)
Browse...
Create Seurat Object
Create Seurat Object from 10X H5
Select 10X H5 file
Browse...
CreateSeuratObject Parameters
min.cells
min.features
Project Name
Assay Name
names.field
names.delim
Upload Metadata (CSV, optional)
Browse...
Create Seurat Object
Reorder Metadata Factor Levels
Select Metadata Column:
nCount_RNA
nFeature_RNA
Order Factor Levels:
Reverse Order
Apply Order
Drop Levels with Zero Values
Merge Seurat Objects
Name for merged object:
Merge Objects
Current Seurat Objects and Notes
▸
Delete a metadata column
Select metadata column to delete:
Delete Column
▸
Rename a metadata column
Select metadata column to rename:
New column name:
Rename Metadata Column
▸
Create new metadata column from two columns
Select first column:
Select second column:
Separator:
New column name:
Create New Column
▸
Download Metadata
Download Metadata
▸
If condition
⚠️ The default assay of the object is not joined. Please join layers first.
Join default assay
Create a new column using dynamic conditions
Add Condition
Remove Last Condition
If TRUE value is:
Fixed
Metadata Column
TRUE Value:
TRUE Value Column:
If FALSE value is:
Fixed
Metadata Column
FALSE Value:
FALSE Value Column:
New Metadata Column Name:
Create New Metadata Column
▸
Mutate Metadata
Select metadata column:
Choose mutation mode:
Mutate same column
Create new column
New column name:
Apply Mutation
Save Current Seurat Object
Save Seurat
Preprocessing progress
Executed Code
Visualization Mode:
Single Metadata Column
Two Metadata Columns
Sort order:
Descending
Ascending
Custom
Order Factor Levels:
Y-axis value:
Counts
Proportions
Color Input Mode:
Comma-separated list
Named color vector
Colors (comma-separated):
Paste named color vector:
Update Colors
Plot transparency (alpha):
Show Pie Chart Labels
Remove grid background (clean look)
Rotate X-axis labels (45°)
Download Table
Preview & Download Plot
Custom Order (X-axis):
Custom Order (Groups):
Show bar borders
Bar border color:
Color Input Mode:
Comma-separated list
Named color vector
Colors (comma-separated):
Paste named color vector:
Update Colors
Plot transparency (alpha):
Remove grid background (clean look)
Rotate X-axis labels (45°)
Drop zero-count combinations
Download Table
Preview & Download Plot
Table
Pie Chart
Bar Plot
Table
Pie Chart
Bar Plot
▸
1. Calculate Mitochondrial Percentage
Calculate percent.mt
▸
2. Subset Cells
Combine conditions with:
AND
OR
Add Condition
After subsetting:
Overwrite active object
Keep original (add as new)
New object name (optional):
Run Subset
▸
3. Split Layers
Select Assay:
Select Layer Column:
Split
▸
4. Normalization
Scale Factor:
Method:
LogNormalize
Normalize Data
▸
5. Find Variable Features
Number of features:
Method:
vst
Find Variable Features
▸
6. Scale Data
Scale Data
▸
7. PCA
Assay:
Number of PCs:
Run PCA
▸
8. Integration (MNN)
Method:
FastMNNIntegration
Original Reduction:
New Reduction Name:
Run Integration
Join Layers after integration
Select Assay to Join:
Join
▸
9. Find Neighbors
Reduction:
Dimensions:
Run FindNeighbors
▸
10. UMAP
Reduction:
Dimensions:
UMAP Name:
Run UMAP
▸
11. tSNE
Reduction:
Dimensions:
tSNE Name:
Run tSNE
▸
12. Clustering
Resolution:
Cluster Column Name:
Algorithm:
1 - Louvain
2 - Louvain multilevel
3 - SLM
4 - Leiden
Run Clustering
▸
Downsampling
Number of cells (N):
Sampling mode:
Random from all cells
Same number per group
After downsampling:
Overwrite active object
Keep original (add as new)
New object name (optional):
Run Downsampling
▸
Download Executed Code
Download Code
Preprocessing progress
Executed Code
Annotation Method:
SingleR
Label Transfer (MNN)
Reference Type:
Pre-built (celldex)
Custom Seurat Object
Reference:
HumanPrimaryCellAtlasData
BlueprintEncodeData
DatabaseImmuneCellExpressionData
MonacoImmuneData
NovershternHematopoieticData
ImmGenData
MouseRNAseqData
Label Type:
label.main
label.fine
Reference object:
Reference assay:
Reference slot (layer):
Assay:
Slot:
Metadata column for clusters:
New Column Base Name:
Run SingleR
Download SingleR Results (ZIP)
Transfer labels from a labeled Seurat reference to your active object using FindTransferAnchors + TransferData.
Reference object:
Reference assay:
Reference slot (layer):
Reference label column:
Query assay:
Query slot (layer):
New Column Prefix (for single cell labels):
Run Label Transfer (MNN)
Group by column:
Generate Summary Table
New Column Name (for group-level label):
Download Cluster Summary (CSV)
Select Scoring Method
Choose method:
AddModuleScore
AUCell
AddModuleScore Settings
Select Assay:
Select Slot:
Gene list (one per line or comma-separated):
Name for Module Score (metadata column):
Control genes number (ctrl):
Calculate Module Score
AUCell Settings
Select Assay:
Select Slot:
Gene list (one per line or comma-separated):
Name for AUCell Score (metadata column):
Top % of ranked genes (AUC max rank):
Run AUCell
AUCell calculates per-cell enrichment of gene sets using the area under the recovery curve of ranked genes.
Field of View (FOV):
Default Boundary:
Update Plots
Plot Options
Select plot type:
ImageDimPlot
ImageFeaturePlot
Plot from:
Gene Expression
Metadata Column
Gene to plot:
Metadata column to plot:
Min cutoff (optional):
Max cutoff (optional):
Update Plots
Group by:
▸
Alpha (Transparency)
Cells alpha:
Molecules alpha:
▸
Cell Border
Color
Size
Update Plots
▸
Cell Colors
Color Input Mode:
Comma-separated list
Named color vector
Colors (comma-separated):
Paste named color vector:
Update Plots
▸
Molecule Plot Settings
Select Genes:
Hide molecules
Molecule Color Input Mode:
Comma-separated list
Named color vector
Colors (comma-separated):
Paste named color vector:
Gene Point Size:
Number of Molecules to Display (nmols):
Update Plots
Show scale bar
Scale bar (pixels):
Scale bar (µm):
Update Plots
Show Axes
X-Intercepts (comma-separated):
Y-Intercepts (comma-separated):
Zoom In
Update Plots
▸
Draw rectangles
Select FOV(s) to load coordinates:
Load Coordinates from FOV(s)
Reset
X ranges (comma-separated xmin-xmax pairs)
Y ranges (comma-separated ymin-ymax pairs)
Colors (comma-separated)
Line Type
solid
dashed
dotted
Line Size
Fill Color (all rectangles)
Fill Transparency (alpha):
▸
Label cells by proximity
Select metadata column:
Select FOV(s):
Select All
Radius (pixels):
Radius (µm):
New column name (optional):
Run Proximity Labeling
Interactive plot
Feature Statistics
Feature type:
Gene
Metadata
Select plot type:
DimPlot
FeaturePlot
VlnPlot
DotPlot
Group by:
Split by:
None
Colors (comma separated):
Point size:
Raster
Show labels
Label size:
Label color:
Label box
Repel labels
Point transparency (alpha):
Reduction:
Columns for split plot:
Plot
Feature 1 source:
Gene
Metadata
Feature 1:
Add second feature
Feature 2 source:
Gene
Metadata
Feature 2:
Assay:
Slot:
Reduction:
Point size:
Raster
Split by:
None
Show labels
Label size:
Label color:
Repel labels
Columns for split plot:
Point transparency (alpha):
Order points by expression
Min cutoff:
Max cutoff:
Colors (comma separated):
Blend (requires 2 features)
Blend threshold:
Plot
Genes:
Numeric Metadata:
Group by:
Split by:
None
Select Assay:
Select Slot:
Y max:
Point size:
Colors (comma separated):
Alpha:
Same Y limits
Number of columns:
Stack
Flip
Plot
Gene(s):
Idents Column:
None
Split By:
None
Colors (comma separated):
Reset Colors
Scale DotPlot
Dot scale:
Plot
▸
FindAllMarkers Options
⚠️ The default assay of the object is not joined. Please join layers first.
Join default assay
Analysis name:
Groups to compare:
Assay:
Slot:
Test:
wilcox
wilcox_limma
bimod
roc
t
negbinom
poisson
LR
MAST
DESeq2
logfc.threshold:
min.pct:
min.diff.pct:
Only positive markers
Max cells per ident:
min.cells.feature:
min.cells.group:
Features to test:
All genes
Specific genes
Select Genes:
Run FindAllMarkers
Reset to Defaults
▸
FindMarkers Options
⚠️ The default assay of the object is not joined. Please join layers first.
Join default assay
Analysis name:
Grouping column:
Assay:
Slot:
Test:
wilcox
wilcox_limma
bimod
roc
t
negbinom
poisson
LR
MAST
DESeq2
logfc.threshold:
min.pct:
min.diff.pct:
Max cells per ident:
min.cells.feature:
min.cells.group:
Features to test:
All genes
Specific genes
Select Genes:
Run FindMarkers
Reset to Defaults
▸
Multi-Group FindMarkers (two-column comparison)
Comparison column:
Stratify by column:
Analysis base name (optional):
Run Multi-Comparison
Download ZIP
▸
Merge DEGs
Upload CSV/TSV files
Browse...
Headers should include: key, logFC, p-value (order configurable below).
Key column index
Fold-change column index
P-value column index
Fold-change cutoff (abs ≥)
P-value threshold (≤)
Output key column name
Show blanks instead of NA (affects CSV)
Merge
Clear
Download ZIP (merged + stats)
Seurat Marker Analysis Manager
Clear Table
Download All Analyses (ZIP)
Select Analysis:
Download CSV
Delete Analysis
Download Table
▸
Read CellChat Object
Upload CellChat RDS File
Browse...
Name for Uploaded Object:
▸
Construct CellChat Object
CellChat Object Construction
Select Seurat Object:
Assay:
Slot (layer):
Metadata column (group by):
Database species:
Human
Mouse
Zebrafish
Interaction Type:
All
Secreted Signaling
ECM-Receptor
Cell-Cell Contact
Non-protein Signaling
Compute Communication Probability Using:
triMean
truncatedMean
Trim fraction (0–0.25):
Analysis Name:
Create CellChat Object
Download All Results (ZIP)
Generate Pathway Plots
Download Pathway Plots (ZIP)
▸
Compare Two CellChat Objects
Select Two Objects for Comparison
Select Object 1 (group of interest):
Select Object 2 (Reference):
Comparison Name:
Run Comparison
Download Comparison Results (ZIP)
▸
Visualize Active CellChat Object
Visualization Level
Choose visualization type:
Overall communication
Pathway level
Ligand–Receptor level
Bubble plot
Gene level
Select cell group:
Interaction direction:
From (Source)
To (Target)
Measure:
Count
Weight
Show edge labels
Remove isolated nodes
Arrow width:
Arrow size:
Edge label size:
Vertex label size:
Plot
Select pathway:
Source groups:
Target groups:
Remove isolate nodes
Show edge labels
Arrow width:
Arrow size:
Edge label size:
Vertex label size:
Font size (for heatmap/role):
Plot type:
Aggregate network
Contribution
Heatmap
Signaling Role
Plot
Download raw data
Select pathway:
Select L-R pair:
Source groups:
Target groups:
Layout:
circle
chord
Font size:
Remove isolate nodes
Plot
Select signaling pathways:
Source groups:
Target groups:
Min dot size:
Max dot size:
Remove isolate nodes
Plot
Download bubble data (CSV)
Select signaling:
Enriched only
Plot
Preview & Download Plot
Available CellChat Objects
Active CellChat Object:
Visualizations for Active CellChat Object
Upload & Settings
Upload CSV / TSV / TXT file:
Browse...
File separator:
Comma (,)
Tab (\t)
Space
Define Annotation Lists
List name:
Gene list (one per line or comma-separated):
Add / Update List
Existing Lists
Clear All Lists
Annotate CSV File
Download Annotated File
Defined Annotation Lists
Preview of Uploaded CSV