User Manual
######################

The aim of this documentation is to provide: an introduction to the system structure and main entities, highlight important updates on the data collection compared to the previous system, list of available features and tools, SOPs, important notes and warning, and important links (to SOPs, documentation, literature, ecodebook). 

.. note:: This project is under active development.

.. warning::
   Only authorized users will be able to access the system functionalities.

1. Create an account
******************************************

This section provides information about the different types of users and respective permissions.

.. toctree::
   :maxdepth: 1

   signup

2. Presentation of the workspace / Overview
************************************************

.. toctree::
   :maxdepth: 1

   overview

3. Create
**********************************

.. toctree::
   :maxdepth: 1

   createPatDon

4. Baseline and Follow-up forms, including Samples and PSQ
***************************************************************

.. toctree::
   :maxdepth: 1

   blfup

5. Patient containers
**************************

.. toctree::
   :maxdepth: 1

   patContainer

6. Organ containers
**************************

.. toctree::
   :maxdepth: 1

   OrganCont

6. List of Diagnosis to enter in the STCS
***************************************************

.. toctree::
   :maxdepth: 1

   ListDiag

How to report an issue
******************************

.. toctree::
   :maxdepth: 1

   issue

Minimal Data
*****************

.. toctree::
   :maxdepth: 1

   minimal

HCP
****

.. toctree::
   :maxdepth: 1

   hcp

PSQ
**************

.. toctree::
   :maxdepth: 1

   psq

Donor
*******

.. toctree::
   :maxdepth: 1

   donor

Transplantation
*********************

.. toctree::
   :maxdepth: 1

   transplantation

Patient baseline
*******************

.. toctree::
   :maxdepth: 1

   patientBL

Skin cancer
*************

.. toctree::
   :maxdepth: 1

   skinCancer

Organ
***************

.. toctree::
   :maxdepth: 1

   organ

Infectious Diseases
**********************

.. toctree::
   :maxdepth: 1

   infdis

Treatment
*******************

.. toctree::
   :maxdepth: 1

   treatment

Lab
*******************

.. toctree::
   :maxdepth: 1

   lab

Samples
***********

.. toctree::
   :maxdepth: 1

   biosamples

Data Quality check
************************

.. toctree::
   :maxdepth: 1

   DQC

Billing
**************

.. toctree::
   :maxdepth: 1

   invoicing

Features and Tools
*********************

.. toctree::
   :maxdepth: 1

   features_tools

Metadata
**************

.. toctree::
   :maxdepth: 1

   metadata

Glossary and Abbreviations
********************************

.. toctree::
   :maxdepth: 1

   glossary

Q&A
******

.. toctree::
   :maxdepth: 1

   qa

Tips
********

.. toctree::
   :maxdepth: 1

   tips