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


download

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

                            
                            

                              
filter by
%
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
NOTEred/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.