updating getting started

cornhundred · Jul 18, 2019 · 997eda2 · 997eda2
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diff --git a/docs/_build_html/.doctrees/environment.pickle b/docs/_build_html/.doctrees/environment.pickle
diff --git a/docs/_build_html/.doctrees/getting_started.doctree b/docs/_build_html/.doctrees/getting_started.doctree
diff --git a/docs/_build_html/_sources/getting_started.rst.txt b/docs/_build_html/_sources/getting_started.rst.txt
@@ -3,33 +3,26 @@
 Getting Started
 ---------------
 
-Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps (see :ref:`intro_heatmap_clustergram`).
+Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps (see :ref:`intro_heatmap_clustergram`). This section will provide information on how to interact with the visualization and how to quickly visualize your own data using the :ref:`clustergrammer_web`, :ref:`clustergrammer_widget` and :ref:`clustergrammer2`.
 
-Using Clustergrammer
-====================
-
-Web application
-~~~~~~~~~~~~~~~
-
-* :ref:`clustergrammer_web`: `http://amp.pharm.mssm.edu/clustergrammer`_
+See :ref:`case_studies` for examples of how Clustergrammer can be used to explore and analyze real world data. For developers interested in building their own web page using Clustergrammer, please refer to the :ref:`building_web_page` section.
 
+Using Clustergrammer
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Clustergrammer can be used as a web application :ref:`clustergrammer_web`, Jupyter Widgets (:ref:`clustergrammer2` and :ref:`clustergrammer_widget`) or stand alone JavaScript libraries (:ref:`clustergrammer_gl` and :ref:`clustergrammer_js`). The newer :ref:`clustergrammer2` and `clustergrammer_gl` libraries are built to handle larger datasets such as scRNA-seq data.
 
-Jupyter Widget
-~~~~~~~~~~~~~~~
-
-* :ref:`clustergrammer2`
 
-  * WebGL for larger datasets (e.g. scRNA-seq)
-* :ref:`clustergrammer_widget`
+scRNA-seq 2,700 PBMC Clustergrammer2 Example
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-  * SVG for smaller datasets (e.g. bulk RNA-seq)
+.. raw:: html
 
-JavaScript and Python libraries
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+         <div style="position: relative; padding-bottom: 10px; height: 0; overflow: hidden; max-width: 100%; height: auto;">
 
-* :ref:`clustergrammer_js` and :ref:`clustergrammer_py` libraries
+         <iframe width="560" height="315" src="https://www.youtube.com/embed/BEPspcC7vIY" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
+         </div>
 
-This section will provide information on how to interact with the visualization and how to quickly visualize your own data using the :ref:`clustergrammer_web` and the :ref:`clustergrammer_widget`. See :ref:`case_studies` for examples of how Clustergrammer can be used to explore and analyze real world data. For developers interested in building their own web page using Clustergrammer, please refer to the :ref:`building_web_page` section.
+Single cell RNA-seq (scRNA-seq) is a powerful method to interrogate gene expression across thousands of single cells. This method provides thousands of measurements (single cells) across thousands of dimensions (genes). Clustergrammer2 is used to interactively explore an example dataset of 2,700 PBMCs obtained from `10X Genomics`_. Bulk gene expression signatures of cell types obtained from `CIBERSORT`_ were used to obtain a tentative cell type for each cell. The data and code can be found on GitHub at `clustergrammer2-notebooks`_ and the notebook can be viewed and re-run on the cloud - see below.
 
 Case Studies and Tutorials
 ========================================
@@ -150,6 +143,10 @@ Clustergrammer has been applied to visualize and analyze a wide variety of biolo
 
 .. _`USDA Nutrient Dataset`: http://nbviewer.jupyter.org/github/MaayanLab/USDA_Nutrients_Viz/blob/master/USDA_Nutrients.ipynb
 
+.. _`10X Genomics`: https://www.10xgenomics.com/resources/datasets/
+.. _`CIBERSORT`: https://cibersort.stanford.edu/
+.. _`clustergrammer2-notebooks`: https://github.com/ismms-himc/clustergrammer2-notebooks
+
 .. |intro-notebook| image:: https://img.shields.io/badge/launch-1.0%20Example%20notebook-579ACA.svg?logo=data:image/png;base64,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
     :alt: version
     :target: https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-examples/master?filepath=notebooks%2F1.0_Clustergrammer2_Example_Notebook.ipynb