indeXplorer

(c) Lars Velten Steinmetz lab, EMBL Heidelberg - Launch tutorial - Load default gating scheme: Individual 1

Welcome to the indeXplorer tutorial.
This tutorial will show you how to explore single cell transcriptomic data by a few simple mouse clicks. Press Next to continue.

Next Quit

Updating Plots

Gates are created by clicking into the plots. To create a rectangular gate, click once on the upper left corner, and close the gate by a double click in the lower right corner. For a polygonal gate, click on as many points as you wish and close the gate by double-clicking. To modify an existing gate, type the name of the gate you want to replace and draw it anew.
To store a state, click the button and remember the stateID that will be created 

                    

                  

                  

                  To restore a state, paste an exisiting stateID into the field below and click the button of your choice. Some useful predefined states:
                  
    
                    
  • 
                      defaultI1
                      Contains all gates used in transcriptomics analysis, as well as the populations from the hierarchical clustering. Displays plots for individual 1.
                    
    • 
                  

                  

                    

                      

                        
                        
                      

                    

                    

                      
                      
                    

                  

                  

                  

                    

                      
                        
                        Store figures as pdf
                      
                    

                    

                      

                        
                        
                      

                    

                    

                      

                        
                        
                      

                    

                  

                

              

            

          

        

        

          

            

          

          

            

              

              

            

            

              

            

            

              

                
                

                  
                  
                

              

              

                
                

                  
                  
                

              

            

          

          

            
          

          

            
            

              

                

                  

                    

                      
Updating Plots

                      
                    

                    
                    

                      

                      

                        
                      

                    

                    

                      

                      

                        
                      

                    

                  

                  

                    

                      

                      

                        
                      

                    

                  

                

              

              

                This module performs gene ontology analysis of the genes with the 10% highest/lowest loadings. It may take a moment for the results to appear.
                

                  
                  

                    
                    
                  

                

                

              

              

                

                  To create a gene list, select the number of genes to store and the principle component to use
                  

                    

                      
                      
                    

                  

                  

                    

                      
                      

                        
                        
                      

                    

                  

                  

                    

                      
                      

                        
                        
                      

                    

                  

                  

                    
                  

                

                

                  

                

              

              

                

                  
                  
                

                
              

            

          

        

        

          

            

              

            

            

              

            

            

              

                
                

                  
                  
                

              

              

                
                

                  
                  
                

              

              

                
                

                  
                  
                

              

              

                
                
              

              

                
                

                  
                  
                

              

              

                
                

                  
                  
                

              

              
Correlation

            

          

          

            
            
            

          

          

            
          

        

        

          

            

              
                This is an interface to the MAST package described by Finak et al (
                pubmed
                ) which allows you to identify genes with differenial expression among arbitrary cell populations.
              
            

            
Computations take between one and 10 minutes depending on the number of cells to be analyzed.

          

          

            

              

              
              

              

                
Updating Plots

                
              

              
            

            

              

                Display options
              

              Changing these values changes the display, without re-running the analysis.
              

              

                
                
              

            

          

          

          

            

              

                

                

                  
                

              

            

          

          

            

              Further analysis
            

            

              
              

                
                
              

            

            You can create a gene list from all genes that are displayed as significant in the plot. Gene lists can be further analyzed in the Gene lists panel
            
            You can perform a Gene Ontology enrichment on the genes that are displayed as significant.
            
            

          

          

            

            
              
              Download Result
            
          

        

        

          

            Gene lists are created whenever you perform an analysis. You can also import gene lists through file upload, from Gene Ontology or from select literature resources.
          

          

            You can use Gene Lists to plot mean expression on scatter plots, to create heat maps, to run clustering algorithms or PCA only on some genes etc.
          

          

          

            

              

                
                

                  
                  
                

              

            

            

              

                
                
              

              
            

            

              

            

            

              

            

          

          

          

          

          
            
            Download Genelist