ARResT
  ARResT/

  initialising...
(and best viewed with Google's Chrome)
pipeline temporarily disabled
welcome to the 'processing' panel, an interface to ARResT/Interrogate's pipeline
please log in if you have an account, or ask an administrator to create one for you
[?] set sample cells


select existing or create new analysis
TIP: select a text file in the file tree to show a preview (150 first lines); non-text files are not shown

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


            



run description
PCR steps
primers
purification
sequencing kit
sequencer
protocol modifications

                
              
select|combine feature types {A}|{B}
[?] spike-ins

                            
                            

                              
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








                      

                      

                          
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 to network and lineup

                              

switch to 'advanced' user mode for more
[?] set    max dist ^    &    absorb min >
normalise by [?]



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 nodes with 0 reads.

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

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

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

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

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

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

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

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.

Tracers :: 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.

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




reference: black-outlined, locked for comparison: red-outlined, red may overlap black

sort sequences by
[index]|status distance
reference & aligned sequences
abundance(s)
on: