ARResT
  ARResT/

  initialising...
(and best viewed with Google's Chrome)
pipeline temporarily disabled
Welcome to the 'processing' panel, the interface to the ARResT/Interrogate pipeline.

Log in if you have an account, or ask an administrator (for public 'stations' use contact@arrest.tools) to create one for you.

If you're interested in processing data from EuroClonality-NGS SOPs for marker identification and clonality assessment, after you log in with a suitable account, switch to 'EC-NGS' (EuroClonality-NGS) user modes (top-left corner).
set sample cells: 


drag and drop files
select existing or create new analysis

                  

                

              

              

                

              

            

          

          

            

            

              

                

                  
                  

                    

                      
                    

                    

                      
                    

                    

                      
                    

                    

                      
                    

                  

                

              

              

                

                  use this to manage user files (data and results) stored on the server
                  

                  

                  
                    
                  
                    
                  
                          
                  
                  
                

                

                  
use this to directly select ARResT results stored on the server - need to log in for user-specific storage

                  

                  

                    

                      
                      

                        
                        

                          
                          
                        

                      

                      
                      
                    

                    

                      

                        

                          

                            

                              
                                
                              
                              
                            

                          

                          

                          

                            

                          

                        

                      

                    

                  

                  

                

                

                  use this to upload results created by (.intrg) or saved through (.Rbin) ARResT
                  

                  

                  

                

                

                  use this to upload one or more IMGT/HighV-QUEST summary files, which will be processed by us to make them compatible with ARResT/Interrogate
                  

                  

                  

                    
                    

                      
                      
                    

                    

                      

                    

                  

                

                

                  use this to upload any tab-delimited table with any number of columns but at least two on top of the required 'sample' and 'size' columns
                                         - see example
                  

                  

                  

                    

                      
                      

                        
                        
                      

                      

                        

                      

                    

                  

                

                

                  use this to directly select ARResT results stored on the server - need to log in for user-specific storage
                  

                  

                  
                  

                    
                    

                      
                      
                    

                  

                

              

            

            

              

              

                

                

                

                

              

            

            

              

            

            

              

                
                

                  

                    
                  

                

              

            

            

              

                

                  
                

              

            

            

              

                
              

              

                
              

            

            

              

              

                
                

                  
                  
                  
                

              

            

            

            

            

            

              

                

                  

                    run description
                    

                  

                  

                    PCR steps
                    

                    primers
                    

                  

                  

                    purification
                    

                  

                  

                    sequencing kit
                    

                    sequencer
                    

                  

                  

                    protocol modifications
                    

                  

                

              

            

            

              

                
                

                  

                    

                      

                        

                        

                        

                          
                            
                          
                          
                        

                      

                      

                        

                          

                        

                        

                          
                          

                            
                            
                          

                        

                      

                      

                        

                      

                    

                    

                  

                  

                    

                  

                  

                    

                  

                  

                    

                  

                

              

            

            

              

            

          

          

            

            

              

                

                  

                

              

              

                

                  

                    

                      
                        
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                          select|combine feature types {A}|{B}
                          

                            

                              

                                
                                

                                  
                                  
                                

                              

                            

                            

                              

                                
                                

                                  
                                  
                                

                              

                            

                          

                          

                            

                              

                                

                                  

                                    
                                    

                                      

                                        

                                          
                                        

                                      

                                    

                                    

                                      

                                        

                                          
                                        

                                      

                                    

                                  

                                

                                

                                  

                                    |cells
                                    

                                      
                                      
                                    

                                  

                                

                              

                            

                          

                          

                            
                          

                        

                        

                          

                            

                            
                            

                            

                              

                                

                              

                              

                                
                              

                            

                          

                        

                      

                    

                  

                

                

                  

                    

                      

                        

                          

                            

                            

                              

                                
                                

                                  
                                  
                                

                              

                            

                          

                          

                            

                              

                                
filter by

                                

                                  

                                    
                                    
                                  

                                

                                
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filter top

                              

                                

                                  
                                  
                                

                              

                              
features per sample

                            

                            

                          

                          

                            
                          

                        

                        

                          

                            

                              

                              
                            

                            
                            

                            

                              

                                

                              

                              

                                
                              

                            

                          

                        

                        

                          

                            
                              
                              
                            
                            
                          

                        

                      

                    

                  

                

              

            

            

              

                

                  

                    

                      

                        
                      

                    

                  

                

              

              

                

                  

                    

                      

                        

                        

                      

                      

                        

                        

                      

                      

                        

                        

                      

                      

                        

                          

                            
                          

                        

                        

                          
   click sample-sample for feature diffs

                        

                        

                          

                            
                          

                        

                      

                      

                        

                        

                      

                    

                    

                      

                        

                          
                          

                            
                            
                          

                        

                      

                      

                        

                          
                          

                            
                            
                          

                        

                      

                      

                        

                          
                          
                        

                      

                      

                        

                          
                          
                        

                      

                      

                        

                          
                          
                        

                      

                      

                        

                          

                            

                              

                                

                                  

                                    
                                  

                                

                              

                            

                            

                              
                            

                          

                          

                            

                            

                              
                              
                            

                            

                              

                                
                              

                            

                          

                        

                      

                    

                    

                      

                        

                        
                      

                      

                        

                          
                          
                        

                      

                      

                        

                          

                            

                              

                                

                                  
                                

                              

                            

                          

                          

                            
                          

                        

                        

                          

                          

                            
                            
                          

                          

                            

                              
                            

                          

                        

                      

                    

                    

                      

                        

                          select  polyclonal  sample(s)
                          

                            
                            

                              
                              
                            

                          

                        

                      

                      

                        

                          

                            
                              set sample|feature cluster thres 
                              
                              
                            
                            

                              

                                

                                  
                                  
                                

                              

                              

                                

                                  
                                  
                                

                              

                            

                          

                        

                      

                    

                    

                      

                        

                          

                            

                              
                              
                              
                            

                          

                        

                        

                          

                            

                              
                              

                                
                                
                              

                            

                          

                          

                            

                              
                              

                                
                                
                              

                            

                          

                          

                            

                              
                              

                                
                                
                              

                            

                          

                        

                        

                          

                            

                              
                                
                                
                              
                              
                            

                          

                          

                            

                              
                                
                                
                              
                              
                            

                          

                          
                        

                        

                          

                            
                            
                          

                          

                            
                            
                          

                          

                            

                              

                                
                                
tips and notes

                              

                              

                              not all functionalities may be available in all 'user modes'

                                                                    tables

                                                                    NOTE: color-code: yellow = lowly abundant features ~ blue = highly abundant features ~ grey = missing features    
                                                                    TIP: left-click to select cell(s)    
                                                                    NOTE: (pre-)filtered features are not selectable    
                                                                    


                                                                    lines

                                                                    TIP: left-click and drag to zoom-in    
                                                                    TIP: left-click on feature in legend to show/hide them    
                                                                    TIP: left-click on a line to (un)highlight it    
                                                                    


                                                                    bars

                                                                    TIP: combine two feature types to plot their shared abundance    
                                                                    NOTE: feature type {B}, if selected, is sorted by abundance    
                                                                    TIP: left-click and drag to zoom-in    
                                                                    TIP: left-click on feature in legend to show/hide them    
                                                                    NOTE: deselecting 'show (pre-)filtered out counts' disables sorting by junction aa length    
                                                                    TIP: 'drill down to feature type' [advanced] and click on a bar to see its fragmentation to that feature type    
                                                                    TIP: 'show differences to sample/group' [advanced] works nicely with bars    
                                                                    TIP: clicking on bars will send some feature types to 'forensics'    
                                                                    


                                                                    bubbles

                                                                    NOTE: feature type {B}, if selected, is sorted alphanumericallye    
                                                                    NOTE: cells with faint X mean that the feature (combo) is either missing from the data or is (pre-)filtered out    
                                                                    NOTE: each sample's bubble is always at the same relative place in each cell    
                                                                    TIP: combine two feature types to plot their shared abundance    
                                                                    TIP: left-click and drag to zoom-in    
                                                                    TIP: left-click on sample names in the legend to show/hide them    
                                                                    NOTE: deselecting samples in the legend doesn't affect working table    
                                                                    


                                                                    heatmaps

                                                                    TIP: left-click to select cells    
                                                                    TIP: left-click and drag to zoom-in    
                                                                    TIP: double-click to zoom-out    
                                                                    TIP: you can transpose (swap axes of) the feature-based heatmaps    
                                                                    TIP: you can control colouring ranges    
                                                                    TIP: you can control clustering thresholds    
                                                                    


                                                                    PCAs

                                                                    NOTE: red/orange-coloured axes indicate uninformative principal components, i.e. treat with caution    
                                                                    NOTE: features are coloured yellow-blue by (mean) abundance    
                                                                    TIP: left-click and drag to select dots    
                                                                    TIP: area of selection can be resized and moved    
                                                                    TIP: left-click out of the selection area to cancel it    
                                                                    NOTE: selected features/samples are listed under the plots
                                                                    
                            

                          

                          
                        

                      

                    

                  

                

              

            

            

              

            

            

              

                
                

                  

                    

                  

                  

                    

                  

                  

                    

                  

                  

                    

                  

                  

                    

                      

                      

                      

                    

                    

                    

                  

                  

                    

                      

                    

                  

                  

                    

                      

                        

                        

                        

                      

                      

                        

                          

                          

                          

                        

                        

                          

                          

                          

                        

                      

                    

                    

                      

                      

                      

                    

                  

                  

                    

                      

                        

                        

                      

                      

                        

                        

                      

                    

                  

                  

                    

                      

                        

                      

                      

                        

                      

                    

                  

                  

                    

                      

                        

                          

                            

                              
                              

                                
                                
                              

                            

                          

                          

                            

                              
                              
                            

                          

                        

                      

                    

                    

                  

                

              

            

          

          

            

              

                

                  ×
                  Nothing to show - use the 'file' panel to select and load existing results or the 'processing' panel to create them.
                

              

            

            

              

                
                  
                
                
You can edit some of the fields by clicking on them - not all fields are editable.

                                         You can resize columns by dragging their boundaries.

                                         filters:
                                         Text fields use search engine logic i.e. looking for fields containing all words (whole or partial). Use "|" or "||" to indicate OR, "-word" to exclude "word". E.g. "rat | bat -cat" will include "rat control" and "big bat" but not "cat catches rat" or "dog is happy".
                                         Numeric fields use logical expressions and operators (<, >, <=, >=, !=, and, or, not) and even functions (abs(), log(), floor(), ceil()). Use "x" as a placeholder !, e.g. "x > 5 and x < 10" keeps values between 5 and 10, while "log(x) > 2" values with natural logarithm greater than 2.

              

              

                
                  
                  
                
                
                  
                  
                
              

              
              

                
                

                  

                    
                    

                      
                      
                    

                    
                    
                  

                  

                    
                    
                    
                    

                    
                  

                

              

            

          

          

            

            

              
              

                

                  

                    

                      

                        
                        

                          
                          
                        

                      

                      

                        

                          

                        

                        
                      

                      

                        

                          

                        

                      

                      

                        

                          

                        

                      

                      

                        

                          

                            
                          

                          

                            

                              

                            

                          

                          

                            

                              

                            

                          

                          

                            
                              
                              download
                            
                          

                        

                      

                    

                    

                      

                        

                        

                                                    Full nucleotide sequences can be retrieved and analysed here,
                                                    when relevant feature types are selected (e.g. clonotypes, junctions) and their features clicked in 'questions'
                                                    - in which case 'forensics' is highlighted.
                                                    There's also a special mode with (auto-)traced clones, if appl.
                                                    Clicking retrieved sequences selects them for download, network analysis, tests.
                                                    

                      

                    

                  

                  

                    

                      

                    

                  

                  

                    

                  

                

                

                  

                    

                      

                        

                          

                            

                              

                              

                                

                                  

                                    
                                  

                                

                              

                              

                                set reference sequence range
                                

                                

                                  

                                    
                                    
                                  

                                

                                
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network quick-guide, tips, notes

                              

                              

                              
                                                                 Each circle (node) is a unique sequence with >=1 reads, each edge is >=1 sequence differences. There are also virtual (vrt) nodes with 0 reads.

                                                                 Concept behind network: maximise distance between unrelated sequences, minimise distance between related ones.

                                                                 Line width represents connection strength, i.e. wide line = strong sequence connection (short distance, strong relatedness), thin line = weak / fragile connection.

                                                                 Line colour can represent several different things, sequence distance by default (blue = low, red = high).

                                                                 Some nodes can be visually distant (with many edges to the root), but still closer than others visually close -> use 'color by distance'.

                                                                 Grey circles and lines are beyond the current distance threshold, see 'sequence selection' drop-down menu.

                                                                 advanced

                                                                 Network processing order: (pre-absorption during pipeline,) distance filter, junction class filter, absorption filter, normalization.

                                                                 Sequences (both active and filtered) might change size when the filter slider is moved, because they are first filtered then absorbed, and absorption is done seperately on active and filtered sequences.

                                                                 Setting distance to filter before creating network will not help you: creating network will (re)calculate threshold and even move the slider.

                                                                 You should expect coloured/active circles after blue (=virtual) circles, but not grey/yellow.

                                                                 clones

                                                                 In general, 'set as clone'->'new' does clone spliting, 'set as clone'->[clone id] does clone merging.

                                                                 Each root is initially assigned to one clone and one color, but you can split it into more clones with 'set as clone'->'new'. In case of tracers, this will also affect 'questions', since a clone tag will be added to the tracer name, and abundances will also change.

                                                                 If you set a selected sequence as a new clone, all sequences closer to your selected sequence than to the root will also be assigned to that clone.

                                                                 Tracers

                                                                 set as clone'->'new' will not reassign clones assigned to other tracer sequences. Use 'set as clone'->[clone id] to reassign those.

                                                                 Initially, you may see circles of different colours. These are sequences within the filtering distance (thus coloured) but also closer to some other root (e.g. tracer) and therefore assign to another clone by default.

                                                                 Clones of other tracer sequences are listed in the table under a black line and are not divided into samples. Therefore they don't show relative values.                                                                                                           		                                                    
                            

                          

                          
                          

                            

                              
                              
                            

                            

                          

                          

                            

                              

                                
                              

                            

                            

                              

                                
                              

                            

                            

                              

                                
                              

                            

                            

                              

                                
                              

                            

                          

                        

                      

                    

                    

                      

                    

                  

                  

                    

                      
sort sequences by

                      

                        

                          
                          

                            
                            
                            
                          

                        

                      

                      

                      

                        

                          

                            
                          

                        

                      

                    

                    

                      

                        

                          

                            
                          

                        

                      

                      

                        

                          
                          
                        

                      

                    

                  

                  

                    
[index] distance

                    
reference & aligned sequences

                    
abundance(s)

                  

                  

                  

                

                

                  

                    

                      

                        on:     
                        

                          
                          

                            
                            
                          

                        

                            
                        
                        
                            
                      

                    

                    

                      

                        

                          
                          

                            

                              
                              

                                
                                
                              

                            

                            

                              
                              

                                
                                
                              

                            

                            

                              
                              

                                
                                
                              

                            

                            

                              
                              

                                
                                
                              

                            

                          

                        

                      

                    

                    

                      

                        

                          

                            
                            

                              
                              
                            

                          

                        

                        

                          

                            
                          

                          

                            
                          

                          

                            
                          

                        

                        

                          

                            

                          

                        

                      

                    

                  

                  
                

              

            

          

          

            Welcome to the reporting panel!
            

            

            

          

          

            
            
            
            

            

              

                

                  

                    
                  

                

                

                  
                  

                    
                    
                  

                

              

              

                

                  

                    

                      
                        cell type
                      
                      
                        

                          
                          

                            
                            
                          

                        

                      
                    

                  

                  

                    
                      
                    
                  

                

              

              

                

                  

                    

                      

                        
                        
                      

                    

                    
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                        download