Protocols
+++++++++

Links for two user-friendly protocols for inferring tree-shaped single-cell trajectories and pseudotime from single-cell transcriptomics data with ``Totem`` can be found below: **QuickStart** and **GuidedStart**. **QuickStart** provides a simple and practical example, whereas the **GuidedStart** protocol details the analysis step-by-step.

All the analyses can be fully reproduced in Linux, MacOS, and Windows OS (amd64 architecture) with >8Gb of RAM using the provided docker image distributed with notebooks, scripts, and data in Docker Hub (``elolab/repro-totem-ti``). 

See the schematic figure below which describes and compares the main step protocols.

.. figure:: _build/html/_images/figure_1.jpg

QuickStart
==========

..
  _The **QuickStart** vignette corresponding to the R markdown notebook ``QuickStart_Totem.Rmd``: `page <QuickStart_Totem.html>`_. 

.. raw:: html

    <embed>
    <p>
    The <b>QuickStart</b> vignette corresponding to the R markdown notebook <code>QuickStart_Totem.Rmd</code>: <a href="vignettes/QuickStart_Totem.html" target="_blank">page</a>. 
    </p>    
    </embed>

----

GuidedStart
===========

..
  _The **GuidedStart** vignette corresponding to the R markdown notebook ``GuidedStart_Totem.Rmd``: `page <GuidedStart_Totem.html>`_.

.. raw:: html

    <embed>
    <p>
    The <b>GuidedStart</b> vignette corresponding to the R markdown notebook <code>GuidedStart_Totem.Rmd</code>: <a href="vignettes/GuidedStart_Totem.html" target="_blank">page</a>.
    </p>    
    </embed>