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updating case studies
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cornhundred committed Jul 17, 2019
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Expand Up @@ -9,6 +9,9 @@ Clustergrammer was developed to visualize high-dimensional biological data (e.g.
Single Cell Gene Expression 2,700 PBMC
=======================================

.. image:: https://img.shields.io/badge/launch-3.0_2700_PBMC_scRNAseq-579ACA.svg?logo=data:image/png;base64,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
:target: https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb

.. raw:: html

<div style="position: relative; padding-bottom: 10px; height: 0; overflow: hidden; max-width: 100%; height: auto;">
Expand All @@ -19,15 +22,13 @@ Single Cell Gene Expression 2,700 PBMC
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.


View Interactive Notebook
View Notebook
~~~~~~~~~~~~~~~~~~~~~~~~~~
The interactive pre-run notebook can be viewed on NBVIewer.

* NBViewer: `NBViewer-2700`_.
View the interactive notebook using NBViewer: `NBViewer-2700`_.

Run Notebook on the Cloud
Run Notebook
~~~~~~~~~~~~~~~~~~~~~~~~~~
This notebook can be re-run and modified on the cloud using:
This notebook can be re-run and modified on the cloud using `MyBinder`_ and other cloud based notebooks:

* MyBinder: `MyBinder-2700`_
* Kaggle: `Viz-2-700-pbmcs-with-cell-type-predictions`_, `Clustergrammer2-2-700-pbmc-notebook`_
Expand Down Expand Up @@ -128,4 +129,5 @@ These examples demonstrate the generality of heatmap visualizations and enable u
.. _`Clustergrammer2-2-700-pbmc-notebook`: https://www.kaggle.com/cornhundred/clustergrammer2-2-700-pbmc-notebook
.. _`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
.. _`Saturn-2700`: https://www.saturncloud.io/published/cornhundred/clustergrammer2-notebooks/notebooks/pbmc_2700_scRNA-seq/1.0_PBMC_2700_scRNA-seq.ipynb
.. _`Saturn-2700`: https://www.saturncloud.io/published/cornhundred/clustergrammer2-notebooks/notebooks/pbmc_2700_scRNA-seq/1.0_PBMC_2700_scRNA-seq.ipynb
.. _`MyBinder`: https://gke.mybinder.org/
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Expand Up @@ -87,8 +87,8 @@
<li class="toctree-l1"><a class="reference internal" href="getting_started.html">Getting Started</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Case Studies and Tutorials</a><ul>
<li class="toctree-l2"><a class="reference internal" href="#single-cell-gene-expression-2-700-pbmc">Single Cell Gene Expression 2,700 PBMC</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#view-interactive-notebook">View Interactive Notebook</a></li>
<li class="toctree-l3"><a class="reference internal" href="#run-notebook-on-the-cloud">Run Notebook on the Cloud</a></li>
<li class="toctree-l3"><a class="reference internal" href="#view-notebook">View Notebook</a></li>
<li class="toctree-l3"><a class="reference internal" href="#run-notebook">Run Notebook</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#cancer-cell-line-encyclopedia-gene-expression-data">Cancer Cell Line Encyclopedia Gene Expression Data</a></li>
Expand Down Expand Up @@ -180,20 +180,18 @@
<p>Clustergrammer was developed to visualize high-dimensional biological data (e.g. genome-wide expression data), but it can also generally be applied to any high-dimensional data. Below are links to several case studies and examples using Clustergrammer to explore high-dimensional data. All examples are below are publically available through GitHub.</p>
<div class="section" id="single-cell-gene-expression-2-700-pbmc">
<span id="try-clustergrammer2-2700"></span><h2>Single Cell Gene Expression 2,700 PBMC<a class="headerlink" href="#single-cell-gene-expression-2-700-pbmc" title="Permalink to this headline"></a></h2>
<a class="reference external image-reference" href="https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb"><img 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src="https://img.shields.io/badge/launch-3.0_2700_PBMC_scRNAseq-579ACA.svg?logo=data:image/png;base64,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" /></a>
<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/f-snXe2Bn9Q" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
</div><p>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 <a class="reference external" href="https://www.10xgenomics.com/resources/datasets/">10X Genomics</a>. Bulk gene expression signatures of cell types obtained from <a class="reference external" href="https://cibersort.stanford.edu/">CIBERSORT</a> were used to obtain a tentative cell type for each cell. The data and code can be found on GitHub at <a class="reference external" href="https://github.com/ismms-himc/clustergrammer2-notebooks">clustergrammer2-notebooks</a> and the notebook can be viewed and re-run on the cloud - see below.</p>
<div class="section" id="view-interactive-notebook">
<h3>View Interactive Notebook<a class="headerlink" href="#view-interactive-notebook" title="Permalink to this headline"></a></h3>
<p>The interactive pre-run notebook can be viewed on NBVIewer.</p>
<ul class="simple">
<li>NBViewer: <a class="reference external" href="https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_10X_Genomics_2700_Dataset_NBViewer.ipynb">NBViewer-2700</a>.</li>
</ul>
<div class="section" id="view-notebook">
<h3>View Notebook<a class="headerlink" href="#view-notebook" title="Permalink to this headline"></a></h3>
<p>View the interactive notebook using NBViewer: <a class="reference external" href="https://nbviewer.jupyter.org/github/ismms-himc/clustergrammer2-notebooks/blob/master/notebooks/3.0_10X_Genomics_2700_Dataset_NBViewer.ipynb">NBViewer-2700</a>.</p>
</div>
<div class="section" id="run-notebook-on-the-cloud">
<h3>Run Notebook on the Cloud<a class="headerlink" href="#run-notebook-on-the-cloud" title="Permalink to this headline"></a></h3>
<p>This notebook can be re-run and modified on the cloud using:</p>
<div class="section" id="run-notebook">
<h3>Run Notebook<a class="headerlink" href="#run-notebook" title="Permalink to this headline"></a></h3>
<p>This notebook can be re-run and modified on the cloud using <a class="reference external" href="https://gke.mybinder.org/">MyBinder</a> and other cloud based notebooks:</p>
<ul class="simple">
<li>MyBinder: <a class="reference external" href="https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb">MyBinder-2700</a></li>
<li>Kaggle: <a class="reference external" href="https://www.kaggle.com/cornhundred/viz-2-700-pbmcs-with-cell-type-predictions">Viz-2-700-pbmcs-with-cell-type-predictions</a>, <a class="reference external" href="https://www.kaggle.com/cornhundred/clustergrammer2-2-700-pbmc-notebook">Clustergrammer2-2-700-pbmc-notebook</a></li>
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Expand Up @@ -9,6 +9,9 @@ Clustergrammer was developed to visualize high-dimensional biological data (e.g.
Single Cell Gene Expression 2,700 PBMC
=======================================

.. image:: https://img.shields.io/badge/launch-3.0_2700_PBMC_scRNAseq-579ACA.svg?logo=data:image/png;base64,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
:target: https://mybinder.org/v2/gh/ismms-himc/clustergrammer2-notebooks/master?filepath=notebooks%2F3.0_2700_PBMC_scRNA-seq.ipynb

.. raw:: html

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Expand All @@ -19,15 +22,13 @@ Single Cell Gene Expression 2,700 PBMC
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.


View Interactive Notebook
View Notebook
~~~~~~~~~~~~~~~~~~~~~~~~~~
The interactive pre-run notebook can be viewed on NBVIewer.

* NBViewer: `NBViewer-2700`_.
View the interactive notebook using NBViewer: `NBViewer-2700`_.

Run Notebook on the Cloud
Run Notebook
~~~~~~~~~~~~~~~~~~~~~~~~~~
This notebook can be re-run and modified on the cloud using:
This notebook can be re-run and modified on the cloud using `MyBinder`_ and other cloud based notebooks:

* MyBinder: `MyBinder-2700`_
* Kaggle: `Viz-2-700-pbmcs-with-cell-type-predictions`_, `Clustergrammer2-2-700-pbmc-notebook`_
Expand Down Expand Up @@ -128,4 +129,5 @@ These examples demonstrate the generality of heatmap visualizations and enable u
.. _`Clustergrammer2-2-700-pbmc-notebook`: https://www.kaggle.com/cornhundred/clustergrammer2-2-700-pbmc-notebook
.. _`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
.. _`Saturn-2700`: https://www.saturncloud.io/published/cornhundred/clustergrammer2-notebooks/notebooks/pbmc_2700_scRNA-seq/1.0_PBMC_2700_scRNA-seq.ipynb
.. _`Saturn-2700`: https://www.saturncloud.io/published/cornhundred/clustergrammer2-notebooks/notebooks/pbmc_2700_scRNA-seq/1.0_PBMC_2700_scRNA-seq.ipynb
.. _`MyBinder`: https://gke.mybinder.org/

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