ABseq App

A resource of gene and surface protein expression in human bone marrow
Citation: Triana S, Vonficht D, Jopp-Saile L, et al. Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states. bioRxiv; 2021. DOI: 10.1101/2021.03.18.435922.

Contact: Sergio Triana, at EMBL Heidelberg, Haas Lab at DKFZ, HI-STEM, BIH, Charité and BIMSB-MDC and Velten lab at CRG

Please use Google Chrome when running the app and wait a couple of minutes while the data loads, in the meantime you can check the following tutorial video.

MOFA-UMAP
This UMAP was calculated using the MOFA dimensions obtained from the antibody and RNA layers 

            

            

              

            

            

              

            

            

              

            

          

          

            

              

            

            

              

            

          

          

            

              

            

          

          

            

              

            

          

        

        

          

            

              

                
                

                  
                  
                

              

            

          

          

            

              

            

            

              

            

            

              

                
                

                  

                    
                  

                  

                    
                  

                

              

            

            

              
            

          

          

            

              Volcano Plot
            

            

              Differential expression result
              

            

          

          

            

              

            

            

              
              

                































                

                

              

            

          

          

            

              
                
                Download DE table
              
            

          

        

        

          Here you can modify the threshold used for every antibody. The default value is the OTSU calculated threshold. These thresholds are used for the calculation of gating schemes using the `tree based` method in the `Calculate scheme` tab and the scheme option in the `Visualisation` tab
          

            

              

            

            

              

                
                

                  
                  
                

                

                  

                

              

            

          

          

            

              

            

            

              
            

            

              

                
                

                  

                    
                  

                  

                    
                  

                

              

            

          

          

            

              

            

            

              

            

          

          

            

              
                
                Download Threshold File (CSV)
              
            

          

        

        

          
            Please select either,
            the Hypergate algorithm
            by Becht et al., 2019 or (Tree Based) a decision three approach using OTSU calculated thresholds, (Tree Based Manual) a tree based approach using the threshold modified by yourself in the `threshold` tab or (Tree based Continous) a tree based approach where the tree algoritm selects the thresholds
          
          

          

          

            

              

                
                

                  
                  
                  
                  
                

              

            

          

          

            

              

            

            

              

            

            

              
            

          

          

            

              

            

            

              

            

            

              

            

          

          

            

              

                































                

                

              

            

            

              

            

          

          

            

              

            

            

              

            

            

              

            

          

          

            

              

            

            

              

            

            

              

            

          

          

            

              

            

            

              

            

            

              

            

          

          

            

              

            

            

              

            

            

              

            

          

        

        

          

            

              MOFA-UMAP
              

              This UMAP was calculated using the MOFA dimensions obtained from the antibody and RNA layers
            

            

              Fate Bias
              

              This plot show the fate bias of the selected trajectory
            

            

              

            

          

          

            

              

            

            

              

            

          

          

            

              Expression in the pseudotime
              

              These plots show the expression of a feature throught the pseudotime of each trajectory