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| Original file line number | Diff line number | Diff line change |
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| Tutorials | ||
| ========= | ||
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| ---------- | ||
| Clustering | ||
| ---------- | ||
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| Currently, for getting started, we recommend `Scanpy's reimplementation <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170505_seurat/seurat.ipynb>`__ of Seurat's [Satija15]_ clustering tutorial 2700 PBMCs from 10x Genomics, containing preprocessing, clustering and the identification of cell types via known marker genes. | ||
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| You might compare this to `clustering 68K PBMCs <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170503_zheng17/zheng17.ipynb>`__ as it would be done in Cell Ranger [Zheng17]_. | ||
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| .. raw:: html | ||
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| <img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/filter_genes_dispersion.png" style="width: 100px"><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"> | ||
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| -------------------- | ||
| Trajectory Inference | ||
| -------------------- | ||
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| For trajectory inference on complex datasets, we offer several examples `here <https://github.com/theislab/paga>`__. Get started `here <https://nbviewer.jupyter.org/github/theislab/paga/blob/master/blood/paul15/paul15.ipynb>`__ for the following result on hematopoiesis. | ||
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| .. raw:: html | ||
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| <img src="http://www.falexwolf.de/img/paga_paul15.png" style="width: 450px"> | ||
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| You can extend this to multi-resolution analyses of whole animals, such as `here <https://nbviewer.jupyter.org/github/theislab/paga/blob/master/planaria/planaria.ipynb>`__. | ||
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| .. raw:: html | ||
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| <img src="http://www.falexwolf.de/img/paga_planaria.png" style="width: 350px"> | ||
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| The PAGA method behind this is described `here <https://rawgit.com/falexwolf/paga_paper/master/paga.pdf>`__ and can be cited using this `doi <https://doi.org/10.1101/208819>`__. As a reference for simple pseudotime analyses, we provide the diffusion pseudotime analyses of [Haghverdi16]_ for two hematopoiesis datasets: `here <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170502_paul15/paul15.ipynb>`__ for [Paul15]_ and `here <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170501_moignard15/moignard15.ipynb>`__ for [Moignard15]_. | ||
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| ----------------- | ||
| Further Tutorials | ||
| ----------------- | ||
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| Regressing out cell cycle | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
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| See this `notebook <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/180209_cell_cycle/cell_cycle.ipynb>`__. | ||
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| Scaling Computations | ||
| ~~~~~~~~~~~~~~~~~~~~ | ||
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| .. raw:: html | ||
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| <img src="http://falexwolf.de/img/scanpy_usage/170522_visualizing_one_million_cells/tsne_1.3M.png" style="width: 120px; margin: -100px 50px 0px 0px" align="right"> | ||
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| Visualize and cluster 1.3M neurons from 10x Genomics `here <https://github.com/theislab/scanpy_usage/tree/master/170522_visualizing_one_million_cells>`__. | ||
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| Simulations | ||
| ~~~~~~~~~~~ | ||
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| Simulating single cells using literature-curated gene regulatory networks [Wittmann09]_. | ||
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| .. raw:: html | ||
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| <img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/timeseries.png" style="width: 200px; margin: -15px 0px 0px 0px" align="right"><img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/draw_graph.png" style="width: 100px; margin: -15px 0px 0px -100px" align="right"> | ||
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| - `notebook <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170430_krumsiek11/krumsiek11.ipynb>`__ for myeloid differentiation | ||
| - `notebook <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170430_krumsiek11/toggleswitch.ipynb>`__ for simple toggleswitch | ||
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| Images | ||
| ~~~~~~ | ||
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| See a pseudotime-based vs. deep-learning based reconstruction of cell cycle from image data `here <https://github.com/theislab/scanpy_usage/tree/master/170529_images>`__ [Eulenberg17]_. | ||
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| .. | ||
| 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 `David P. Cook <https://twitter.com/DavidPCook>`__. Data by `Tabula Muris Consortium <https://www.biorxiv.org/content/early/2017/12/20/237446>`__. | ||
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| This file has moved to https://scanpy.readthedocs.io/en/latest/tutorials.html. |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| Tutorials | ||
| ========= | ||
|
|
||
|
|
||
| ---------- | ||
| Clustering | ||
| ---------- | ||
|
|
||
| For getting started, we recommend `Scanpy's reimplementation <https://scanpy-tutorials.readthedocs.io/en/latest/pbmc3k.html>`__ of Seurat's [Satija15]_ clustering tutorial for 3K PBMCs from 10x Genomics, containing preprocessing, clustering and the identification of cell types via known marker genes. | ||
|
|
||
| You might compare this to `clustering 68K PBMCs <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170503_zheng17/zheng17.ipynb>`__ as it would be done in Cell Ranger [Zheng17]_. | ||
|
|
||
| .. raw:: html | ||
|
|
||
| <img src="http://falexwolf.de/img/scanpy_usage/170505_seurat/filter_genes_dispersion.png" style="width: 100px"><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"> | ||
|
|
||
|
|
||
| -------------------- | ||
| Trajectory Inference | ||
| -------------------- | ||
|
|
||
| For trajectory inference on complex datasets, we offer several examples `here <https://github.com/theislab/paga>`__. Get started `here <https://nbviewer.jupyter.org/github/theislab/paga/blob/master/blood/paul15/paul15.ipynb>`__ for the following result on hematopoiesis. | ||
|
|
||
| .. raw:: html | ||
|
|
||
| <img src="http://www.falexwolf.de/img/paga_paul15.png" style="width: 450px"> | ||
|
|
||
| You can extend this to multi-resolution analyses of whole animals, such as `here <https://nbviewer.jupyter.org/github/theislab/paga/blob/master/planaria/planaria.ipynb>`__. | ||
|
|
||
| .. raw:: html | ||
|
|
||
| <img src="http://www.falexwolf.de/img/paga_planaria.png" style="width: 350px"> | ||
|
|
||
| The PAGA method behind this is described `here <https://rawgit.com/falexwolf/paga_paper/master/paga.pdf>`__ and can be cited using this `doi <https://doi.org/10.1101/208819>`__. As a reference for simple pseudotime analyses, we provide the diffusion pseudotime analyses of [Haghverdi16]_ for two hematopoiesis datasets: `here <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170502_paul15/paul15.ipynb>`__ for [Paul15]_ and `here <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170501_moignard15/moignard15.ipynb>`__ for [Moignard15]_. | ||
|
|
||
|
|
||
| ----------------- | ||
| Further Tutorials | ||
| ----------------- | ||
|
|
||
| Regressing out cell cycle | ||
| ~~~~~~~~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| See this `notebook <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/180209_cell_cycle/cell_cycle.ipynb>`__. | ||
|
|
||
|
|
||
| Scaling Computations | ||
| ~~~~~~~~~~~~~~~~~~~~ | ||
|
|
||
| .. raw:: html | ||
|
|
||
| <img src="http://falexwolf.de/img/scanpy_usage/170522_visualizing_one_million_cells/tsne_1.3M.png" style="width: 120px; margin: -100px 50px 0px 0px" align="right"> | ||
|
|
||
| Visualize and cluster 1.3M neurons from 10x Genomics `here <https://github.com/theislab/scanpy_usage/tree/master/170522_visualizing_one_million_cells>`__. | ||
|
|
||
|
|
||
| Simulations | ||
| ~~~~~~~~~~~ | ||
|
|
||
| Simulating single cells using literature-curated gene regulatory networks [Wittmann09]_. | ||
|
|
||
| .. raw:: html | ||
|
|
||
| <img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/timeseries.png" style="width: 200px; margin: -15px 0px 0px 0px" align="right"><img src="http://falexwolf.de/img/scanpy_usage/170430_krumsiek11/draw_graph.png" style="width: 100px; margin: -15px 0px 0px -100px" align="right"> | ||
|
|
||
| - `notebook <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170430_krumsiek11/krumsiek11.ipynb>`__ for myeloid differentiation | ||
| - `notebook <https://nbviewer.jupyter.org/github/theislab/scanpy_usage/blob/master/170430_krumsiek11/toggleswitch.ipynb>`__ for simple toggleswitch | ||
|
|
||
|
|
||
| Images | ||
| ~~~~~~ | ||
|
|
||
| See a pseudotime-based vs. deep-learning based reconstruction of cell cycle from image data `here <https://github.com/theislab/scanpy_usage/tree/master/170529_images>`__ [Eulenberg17]_. | ||
|
|
||
|
|
||
| .. | ||
| 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 `David P. Cook <https://twitter.com/DavidPCook>`__. Data by `Tabula Muris Consortium <https://www.biorxiv.org/content/early/2017/12/20/237446>`__. | ||
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|