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Commit ca585c86 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

doc/browser.org: update help, patient database, search box

parent 9a3465bd
...@@ -38,9 +38,10 @@ Otherwise, such .vidjil files can be obtained: ...@@ -38,9 +38,10 @@ Otherwise, such .vidjil files can be obtained:
* First aid * First aid
- Open data by: - Open data by:
- either with “patients”/“open patient” (if you have access to the database) - either with “patients”/“open patient” if you are connected to a patient database
(in this case, there are always some "Demo" datasets for demonstration purposes),
- or with “file”/“import/export”, manually selecting a .vidjil file - or with “file”/“import/export”, manually selecting a .vidjil file
There is always a “LIL-L2” dataset for demonstration purposes.
- You can change the number of displayed clones by moving the slider “number of clones” (menu “filter”). - You can change the number of displayed clones by moving the slider “number of clones” (menu “filter”).
The maximal number of clones that can be displayed depends on the processing step before. The maximal number of clones that can be displayed depends on the processing step before.
...@@ -60,8 +61,8 @@ Otherwise, such .vidjil files can be obtained: ...@@ -60,8 +61,8 @@ Otherwise, such .vidjil files can be obtained:
- system :: system used for analyzing the data. In case of multi-system - system :: system used for analyzing the data. In case of multi-system
data, you can select what system should be displayed. data, you can select what system should be displayed.
- point :: name of the current point (you can change the selected point by clicking on - point :: name of the current point (you can change the selected point by clicking on
another point in the graph). The name can be edited (“...” button). another point in the graph). The name can be edited (“edit”).
- date :: when the run was performed (manually curated, with “...” button) - date :: when the run was performed (edit either with “...”, or with the database, on the patient tab)
- segmented :: number of reads where Vidjil found a CDR3, for that point. - segmented :: number of reads where Vidjil found a CDR3, for that point.
See [[Number of segmented reads]] below. See [[Number of segmented reads]] below.
- total :: total number of reads for that point - total :: total number of reads for that point
...@@ -81,6 +82,10 @@ Otherwise, such .vidjil files can be obtained: ...@@ -81,6 +82,10 @@ Otherwise, such .vidjil files can be obtained:
The “+” and “-” allow respectively to un-merge or re-merge all clones that have The “+” and “-” allow respectively to un-merge or re-merge all clones that have
already been merged. already been merged.
- Clones can be searched (“search” box) by either their name, their custom name,
or their DNA sequence.
** The graph ** The graph
- The gray areas at the bottom of the graph show, for each point, the resolution (1 read / 5 reads). - The gray areas at the bottom of the graph show, for each point, the resolution (1 read / 5 reads).
...@@ -124,7 +129,7 @@ installation of Vidjil (as on http://rbx.vidjil.org/browser), the ...@@ -124,7 +129,7 @@ installation of Vidjil (as on http://rbx.vidjil.org/browser), the
'patient' menu gives you access to the server. 'patient' menu gives you access to the server.
With authentication, you can add patients, then add either With authentication, you can add patients, then add either
=.fasta=/=.fastq=/=.gz= files or =.clntab= files, then process your =.fasta=, =.fastq=, =.gz= or =.clntab= files, then process your
runs and save the results of your analysis. runs and save the results of your analysis.
*** Patients *** Patients
......
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