Welcome to the biodiversity explorer app

This interactive app offers you a simple way of analyzing and playing with the microbial commuminty data.

You can explore raw data, merge replicate samples, perform state-of-the-art analysis and find interactive visualizations.

To learn how the app works and what you can do watch a short intro video, check the online manual / tutorial or simply explore on your own.


Demo videos

The intro video will show you the most important functions and basic bahavior:

Link to videos

Manual / Tutorial

The manual explains the behavior and options of each control element and analysis window.

Link to Manual / Tutorial

To detect specialist and generalist different approaches are known. Here indicator species will be detected as specialist. Generalist will be detected by minimal abundance and minimal occurence.

We recommend to restrict the indicator species detection to the top expressed ASV/OTUs only.

Your selection includes the following number of features:

You can select the top x features based on order of your input table. Note: The order of your uploaded data is changed if sorting by mean before selection is active.

You can select most interesting feature by the mean of all samples. To view the distribution of the mean explore the plot below.

There are several concepts of (habitat) specialist or indicator species that slighly differ. Here we use the indicator value detection by Dufrene and Legendre (1997). The analysis requires two inputs: an abundance / count table and groups. The analysis output is two value for each feature (ASV/OTU/MAG): a P-value of statistical significance of enrichment in one of the groups and an indicator value showing the strength of indication for this group (value from 0 to 1), with higher values showing more specific enrichtment for the group. For more examples of how to find specific features or to interprete the results see the tutorial.


                      

                      

                      
                        
                        Download table
                      
                      

                      

                      

                    

                    

                      

                        
                        
                      

                      

                        

                          
                          
                        

                      

                      

                        

                        

                        

                      

                      

                      
                      

                      
Generalist results:

                      

                    

                    

                      

                        

                          
                          
                        

                      

                      

                        

                          
                          
                        

                      

                      

                      
                      

                        
                        

                          

                            

                          

                          

                            

                          

                        

                      

                    

                  

                

              

              

                
Coming soon

              

              

                
Settings

                
Do you want to store your loaded and processed data? This enables automatic 
         loading of the data on next app start.

                

                  
                  

                    

                      
                    

                    

                      
                    

                  

                

                

                  
                  

                    

                      
ASV / OTU / MAG or other counts table

                      

                        
                        

                          
                          
                        

                        

                          

                        

                      

                      
                      
                      

                      

                      
                    

                    

                      
Taxa table

                      

                        
                        

                          
                          
                        

                        

                          

                        

                      

                      
                      
                      

                      

                      
                    

                    

                      
Samples data table

                      

                        
                        

                          
                          
                        

                        

                          

                        

                      

                      
                      
                      

                      

                      
                    

                    

                      
Coming soon!

                    

                  

                

              

              

                
Show and export tables

                
                

                
Rarefaction

                
                

                
Relative abundance

                
Calculate relative abundance from raw data.

                
                
Apply cutoff for minimal abundance

                
You can apply a cutoff to remove low abundant ASV's or OTU's, 
             e.g. rare biosphere.

                

                  
                  
                

                
                

                
Summarize by taxonomy

                
Coming soon

              

              

                

                  
                  
                

                

                  
                  
                

                

                  
                  

                    
                    
                  

                

                

                  
                  
                

                

                  
                  
                

                

                  
                  

                    
                    
                  

                

                
                

                

                
                
                

                
Table of merged sample. Select row in the table to edit, or create new.

                

                

                
Order samples by drag and drop. Missing samples will be added on saving in 
    there default order.