<commit_before>Examples
--------

Good starting points are the following examples, which build on established results from the literature. All examples are versioned on `GitHub <scanpy_usage_>`__.

.. _scanpy_usage: https://github.com/theislab/scanpy_usage

------------

`Example 1: <17-05-05_>`__ `Seurat's <Seurat_>`__ [Satija15]_ guided clustering `tutorial <http://satijalab.org/seurat/pbmc3k_tutorial.html>`_.

.. raw:: html

   <a href="https://github.com/theislab/scanpy_usage/tree/master/170505_seurat"><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/filter_genes_dispersion.png" style="width: 100px"></a><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/louvain.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/NKG7.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/violin.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/cell_types.png" style="width: 200px">

------------

`Example 2: <17-05-02_>`__ The Diffusion Pseudotime (DPT) analyses of [Haghverdi16]_ for data of [Paul15]_ and [Moignard15]_. Note that DPT has recently been very `favorably discussed`_ by the authors of Monocle_.

.. raw:: html

   <a href="https://github.com/theislab/scanpy_usage/tree/master/170502_haghverdi16"><img src="http://falexwolf.de/img/scanpy_usage/170501_moignard/scatter.png" style="width: 350px"></a><img src="http://falexwolf.de/img/scanpy_usage/170501_moignard/heatmap.png" style="width: 80px">


------------

`Example 3: <17-05-03_>`__ Analyzing 68 000 cells from [Zheng17]_, we find that Scanpy is about a factor 5 to 16 faster and more memory efficient than the `Cell Ranger`_ R kit for secondary analysis.

.. raw:: html

   <a href="https://github.com/theislab/scanpy_usage/tree/master/170503_zheng17"><img src="http://falexwolf.de/img/scanpy_usage/170503_zheng17/speedup.png" style="width: 300px"></a><img src="http://falexwolf.de/img/scanpy_usage/170503_zheng17/scatter.png" style="width: 100px">
   
------------

`Example 4: <17-05-22_>`__ Visualizing 1.3 mio `brain cells <https://support.10xgenomics.com/single-cell-gene-expression/datasets/1M_neurons>`_.

.. raw:: html

   <img src="http://falexwolf.de/img/scanpy_usage/170522_visualizing_one_million_cells/tsne.png" style="width: 120px"><img src="http://falexwolf.de/img/scanpy_usage/170522_visualizing_one_million_cells/diffmap_comps23.png" style="width: 165px">
   
------------

`Example 5: <17-04-30_>`__ Simulating single cells using literature-curated gene regulatory networks [Wittmann09]_; here, myeloid differentiation [Krumsiek11]_.

.. raw:: html

   <img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/timeseries.png" style="width: 200px"><img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/tsne.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/draw_graph.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/diffmap.png" style="width: 100px">
   
------------

`Example 6: <17-04-30_>`__ Pseudotime-based vs. deep-learning based reconstruction of cell cycle from image data [Eulenberg17]_.

.. raw:: html

   <img src="http://falexwolf.de/img/scanpy_usage/170529_images/dpt_DNA_content.png" style="width: 200px">
   
------------

.. _17-04-30: https://github.com/theislab/scanpy_usage/tree/master/170430_krumsiek11
.. _17-05-03: https://github.com/theislab/scanpy_usage/tree/master/170503_zheng17
.. _17-05-02: https://github.com/theislab/scanpy_usage/tree/master/170502_haghverdi16
.. _17-05-05: https://github.com/theislab/scanpy_usage/tree/master/170505_seurat
.. _17-05-22: https://github.com/theislab/scanpy_usage/tree/master/170522_visualizing_one_million_cells

.. _Guided Clustering tutorial: http://satijalab.org/seurat/pbmc3k_tutorial.html
.. _Seurat: http://satijalab.org/seurat
.. _Cell Ranger: https://github.com/10XGenomics/single-cell-3prime-paper/tree/master/pbmc68k_analysis
.. _favorably discussed: https://doi.org/10.1101/110668
.. _Monocle: http://cole-trapnell-lab.github.io/monocle-release/articles/v2.0.0/<commit_msg>added user examples to docs<commit_after>Examples
--------

Good starting points are the following examples, which build on established results from the literature. All examples are versioned on `GitHub <scanpy_usage_>`__.

.. _scanpy_usage: https://github.com/theislab/scanpy_usage

------------

`Example 1: <17-05-05_>`__ `Seurat's <Seurat_>`__ [Satija15]_ guided clustering `tutorial <http://satijalab.org/seurat/pbmc3k_tutorial.html>`_.

.. raw:: html

   <a href="https://github.com/theislab/scanpy_usage/tree/master/170505_seurat"><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/filter_genes_dispersion.png" style="width: 100px"></a><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/louvain.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/NKG7.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/violin.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/cell_types.png" style="width: 200px">

------------

`Example 2: <17-05-02_>`__ The Diffusion Pseudotime (DPT) analyses of [Haghverdi16]_ for data of [Paul15]_ and [Moignard15]_. Note that DPT has recently been very `favorably discussed`_ by the authors of Monocle_.

.. raw:: html

   <a href="https://github.com/theislab/scanpy_usage/tree/master/170502_haghverdi16"><img src="http://falexwolf.de/img/scanpy_usage/170501_moignard/scatter.png" style="width: 350px"></a><img src="http://falexwolf.de/img/scanpy_usage/170501_moignard/heatmap.png" style="width: 80px">


------------

`Example 3: <17-05-03_>`__ Analyzing 68 000 cells from [Zheng17]_, we find that Scanpy is about a factor 5 to 16 faster and more memory efficient than the `Cell Ranger`_ R kit for secondary analysis.

.. raw:: html

   <a href="https://github.com/theislab/scanpy_usage/tree/master/170503_zheng17"><img src="http://falexwolf.de/img/scanpy_usage/170503_zheng17/speedup.png" style="width: 300px"></a><img src="http://falexwolf.de/img/scanpy_usage/170503_zheng17/scatter.png" style="width: 100px">
   
------------

`Example 4: <17-05-22_>`__ Visualizing 1.3 mio `brain cells <https://support.10xgenomics.com/single-cell-gene-expression/datasets/1M_neurons>`_.

.. raw:: html

   <img src="http://falexwolf.de/img/scanpy_usage/170522_visualizing_one_million_cells/tsne.png" style="width: 120px"><img src="http://falexwolf.de/img/scanpy_usage/170522_visualizing_one_million_cells/diffmap_comps23.png" style="width: 165px">
   
------------

`Example 5: <17-04-30_>`__ Simulating single cells using literature-curated gene regulatory networks [Wittmann09]_; here, myeloid differentiation [Krumsiek11]_.

.. raw:: html

   <img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/timeseries.png" style="width: 200px"><img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/tsne.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/draw_graph.png" style="width: 100px"><img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/diffmap.png" style="width: 100px">
   
------------

`Example 6: <17-04-30_>`__ Pseudotime-based vs. deep-learning based reconstruction of cell cycle from image data [Eulenberg17]_.

.. raw:: html

   <img src="http://falexwolf.de/img/scanpy_usage/170529_images/dpt_DNA_content.png" style="width: 200px">
   
------------

.. _17-04-30: https://github.com/theislab/scanpy_usage/tree/master/170430_krumsiek11
.. _17-05-03: https://github.com/theislab/scanpy_usage/tree/master/170503_zheng17
.. _17-05-02: https://github.com/theislab/scanpy_usage/tree/master/170502_haghverdi16
.. _17-05-05: https://github.com/theislab/scanpy_usage/tree/master/170505_seurat
.. _17-05-22: https://github.com/theislab/scanpy_usage/tree/master/170522_visualizing_one_million_cells

.. _Guided Clustering tutorial: http://satijalab.org/seurat/pbmc3k_tutorial.html
.. _Seurat: http://satijalab.org/seurat
.. _Cell Ranger: https://github.com/10XGenomics/single-cell-3prime-paper/tree/master/pbmc68k_analysis
.. _favorably discussed: https://doi.org/10.1101/110668
.. _Monocle: http://cole-trapnell-lab.github.io/monocle-release/articles/v2.0.0/



User Examples
~~~~~~~~~~~~~

January 12, 2018: `Exploring the mouse cell atlas <https://github.com/dpcook/fun_analysis/blob/master/tabula_muris/mouse_atlas_scanpy.ipynb>`_ by `<NAME> <https://twitter.com/DavidPCook>`_. Data by `Tabula Muris Consortium <https://www.biorxiv.org/content/early/2017/12/20/237446>`_.
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