added CITE-seq example to documentation

docs/_build_html/_sources/case_studies.rst.txt

@@ -24,9 +24,30 @@ Single cell RNA-seq (scRNA-seq) is a powerful method to interrogate gene express
 
 View and Run 2,700 PBMC scRNA-seq Notebook
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-* `NBViewer-2700`_
-* `MyBinder-2700`_
-* Kaggle: `Viz-2-700-pbmcs-with-cell-type-predictions`_, `Clustergrammer2-2-700-pbmc-notebook`_
+* `NBViewer scRNA-seq 2700`_
+* `MyBinder scRNA-seq 2700`_
+
+
+CITE-seq 7,800 PBMC
+=======================================
+
+.. image:: https://img.shields.io/badge/launch-CITEseq%207,800%20PBMC-579ACA.svg?logo=data:image/png;base64,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
+   :target: https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F4.1_10K_PBMC_CITE-seq_Visualize_Data.ipynb
+
+.. raw:: html
+
+         <div style="position: relative; padding-bottom: 10px; height: 0; overflow: hidden; max-width: 100%; height: auto;">
+
+         <iframe width="560" height="315" src="https://www.youtube.com/embed/oG9TunM1Bvw" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
+         </div>
+
+CITE-seq (a.k.a feature barcoding from 10X genomics) is a new method that enabels researchers to simultaneously measure gene expression and protein levels in single cells. This notebook uses Clustergrammer2 to interactively explore an example dataset measuring the gene expression and surface marker proteins of 7,800 PBMCs obtained from 10X Genomics. Cell type was assigned based on unbiased hierarchical clustering of cells in surface marker space (ADTs) and transferred to cells in gene expression space. Please see the video tutorial above for more information.
+
+
+View and Run 2,700 PBMC scRNA-seq Notebook
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+* `NBViewer CITE-seq 7800`_
+* `MyBinder CITE-seq 7800`_
 
 Cancer Cell Line Encyclopedia Gene Expression Data
 ==================================================
@@ -123,10 +144,13 @@ These examples demonstrate the generality of heatmap visualizations and enable u
 .. _`10X Genomics`: https://www.10xgenomics.com/resources/datasets/
 .. _`CIBERSORT`: https://cibersort.stanford.edu/
 .. _`clustergrammer2-notebooks`: https://github.com/ismms-himc/clustergrammer2-notebooks
-.. _`Viz-2-700-pbmcs-with-cell-type-predictions`: https://www.kaggle.com/cornhundred/viz-2-700-pbmcs-with-cell-type-predictions
-.. _`Clustergrammer2-2-700-pbmc-notebook`: https://www.kaggle.com/cornhundred/clustergrammer2-2-700-pbmc-notebook
 .. _`MyBinder`: https://gke.mybinder.org/
-.. _`MyBinder-2700`: https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb
-.. _`NBViewer-2700`: https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_10X_Genomics_2700_Dataset_NBViewer.ipynb
+
+.. _`MyBinder scRNA-seq 2700`: https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb
+.. _`NBViewer scRNA-seq 2700`: https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_10X_Genomics_2700_Dataset_NBViewer.ipynb
+
+.. _`MyBinder CITE-seq 7800`: https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F4.1_10K_PBMC_CITE-seq_Visualize_Data.ipynb
+.. _`NBViewer CITE-seq 7800`: https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/4.1_10K_PBMC_CITE-seq_Visualize_Data.ipynb?flush_cache=true
+
 .. _`MyBinder-CCLE`: https://mybinder.org/v2/gh/ismms-himc/clustergrammer2_examples/master?filepath=notebooks%2F2.0_CCLE_Gene_Expression.ipynb
 .. _`NBViewer-CCLE`: https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/2.0_CCLE_Gene_Expression.ipynb?flush_cache=True