Step 1: Upload Your Data




✓ Object Loaded Successfully


                          

                        

                      

                    

                    

                    

                      

                        

                          

                            
                            

                              
                              
                            

                          

                        

                        

                          

                            
                            

                              
                              
                            

                          

                        

                      

                      

                      

                        
Available Metadata Columns:

                        

                      

                      

                      

                      

                        
                      

                    

                  

                

                

                  

                    
Step 2: Configure Data Subset

                    

                      

                        

                          
Subsetting Strategy

                          

                            
                            

                              

                                
                              

                              

                                
                              

                              

                                
                              

                            

                          

                        

                      

                      

                        

                          

                            
Column Selection

                            

                              

                                
                                

                                  
                                  
                                

                              

                              

                            

                            

                              

                                
                                
                              

                              

                            

                          

                        

                      

                    

                    

                    

                      
Current Subset Summary

                      

                    

                    

                    

                    

                      
                      
                    

                  

                

                

                  

                    
Step 3: Load Bimodal Index

                    

                      

                        
                         What is Bimodal Index?
                      

                      

                        The Bimodal Index (BI) measures how well a feature separates cells into two distinct populations.
                      

                      
    
                        
  • 
                          Higher BI values:
                           Clear bimodal distribution with distinct peaks → 
                          Excellent gating candidate
                        
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  • 
                          Lower BI values:
                           Unimodal or uniform distribution → 
                          Poor gating candidate
                        
    • 
                      

                      

                        
                         Tip: BI values can exceed 1.0. Focus on features in the top 5-10% (95th-99th percentile) of your dataset for the best discrimination, regardless of their absolute BI values.
                      

                    

                    

                      

                        

                          

                            
                             Calculate in the app
                          

                          

                            

                              

                                

                                  

                                    
                                  

                                

                                
                                  Faster, but restricts the search to the 
                                  features Seurat already flagged as variable.
                                
                              

                              

                                

                                
                              

                            

                            
                              
                              Fits a two-component mixture to every feature, in C++, 
                              on the cells you selected at Step 2. Typically seconds to 
                              a couple of minutes. Every cell is used — no subsampling — 
                              so the index is exact.
                            
                          

                          

                            

                              
                               The bimodal index cannot be computed on this server.
                              

                                The C++ fit could not be compiled at startup, which 
                                almost always means no C++ compiler is installed. 
                                Install one and restart the app: Rtools on Windows, 
                                xcode-select --install on macOS, or build-essential 
                                on Linux. The R console where the app started shows 
                                the exact error.
                              

                            

                          

                        

                      

                    

                    

                      

                        

                          

                            
✓ Bimodal Index Loaded

                            

                            

                              

                                

                                  
                                  

                                    
                                    
                                  

                                

                              

                              

                                

                                  
                                  
                                

                              

                              

                                
                              

                            

                          

                        

                      

                    

                    

                    

                      

                        

                          

                            

                              
                               Suggested Cutoffs (percentiles):
                            

                            

                            
                              These values represent the BI score at each percentile. 
                              Features above these thresholds are in the top 10%, 5%, or 1% respectively.
                            
                          

                        

                        

                          

                            

                              
                               Selected Features for Gating:
                            

                            

                            These features passed your threshold and will be available for density contour gating in Step 4.
                          

                        

                      

                      

                      

                        

                          

                            
                            

                              
                              
                            

                          

                        

                        

                          

                            

                              
                            

                          

                        

                      

                      
Bimodal Index Distribution

                      
                        This histogram shows the distribution of BI scores across all analyzed features. 
                        The vertical lines indicate percentile cutoffs. Features to the right have higher bimodality.
                      
                      

                      

                      
All Features Ranked by Bimodal Index

                      
                        Browse all features and their BI scores. Click column headers to sort. 
                        Use the search box to find specific genes of interest.
                      
                      

                    

                    

                    

                    

                      

                        
                        
                      

                    

                  

                

                

                  

                    
Step 4: Create Gates by Clicking Contours

                    

                      

                        

                          
Gate Controls

                          

                            
                            

                              
                              
                            

                          

                          

                            

                              
                            

                          

                          

                            
                            

                              
                              
                            

                          

                          

                          
Contour Settings

                          

                            
                            
                          

                          
                            Lower threshold = more contours (less selective)
                            

                            Higher threshold = fewer contours (more selective)
                          
                        

                        

                          
Save Gate

                          

                            
                            
                          

                          
                          
                          

                          
Saved Gates

                          

                          
                        

                      

                      

                        

                          
                          

                            

                              

                              

                                
                                 How to use:
                                
    
                                  
  • Black contour lines show high-density regions for the selected feature
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                                    Click inside any contour boundary
                                     to select all cells within that region
                                  
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  • 
                                    Selected cells will be highlighted in 
                                    yellow
                                  
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  • Review selection in 'Current Selection' panel below
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  • Enter a gate name and click 'Save Selected Cells as Gate'
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  • Use zoom controls to focus on specific regions
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Current Selection

                                    

                                  

                                

                                

                                  

                                    
Contour Statistics (Zoomed)

                                    

                                  

                                

                              

                            

                          

                        

                      

                    

                    

                    

                      

                        
                      

                      

                        
                      

                    

                  

                

                

                  

                    
Step 5: Gate Statistics and Analysis

                    

                      
Gated Cells Distribution

                      

                    

                    

                    

                      

                        

                          
Gate Details

                          

                          

                          

                        

                      

                      

                        

                          
Overlap Analysis

                          

                        

                      

                    

                    

                    

                    

                      
                      
                    

                  

                

                

                  

                    
Step 6: Export and Save Results

                    

                      

                        
                      

                      

                        

                          
                          
Start a New Session

                          

                          
                            Clears the loaded object, the bimodal index results and 
                            all saved gates, and returns to Step 1.
                          
                          

                          
Start Over: