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earmingol committed Nov 19, 2023
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189 changes: 98 additions & 91 deletions documentation/index.html

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19 changes: 17 additions & 2 deletions index.html
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</li>
<li class="toctree-l2"><a class="reference internal" href="#examples">Examples</a>
</li>
<li class="toctree-l2"><a class="reference internal" href="#liana-tensor-cell2cell">LIANA &amp; Tensor-cell2cell</a>
</li>
<li class="toctree-l2"><a class="reference internal" href="#common-issues">Common issues</a>
</li>
<li class="toctree-l2"><a class="reference internal" href="#ligand-receptor-pairs">Ligand-Receptor pairs</a>
Expand Down Expand Up @@ -103,7 +105,7 @@ <h1 id="inferring-cell-cell-interactions-from-transcriptomes-with-cell2cell">Inf
<p><a href="https://pypi.org/project/cell2cell/"><img alt="PyPI Version" src="https://badge.fury.io/py/cell2cell.svg" /></a>
<a href="https://pepy.tech/project/cell2cell"><img alt="Downloads" src="https://pepy.tech/badge/cell2cell/month" /></a></p>
<h2 id="getting-started">Getting started</h2>
<p>Please refer to the <a href="https://earmingol.github.io/cell2cell/">cell2cell website</a>,
<p>Please refer to the <a href="https://cell2cell.readthedocs.org">cell2cell website</a>,
which includes tutorials and documentation</p>
<h2 id="installation">Installation</h2>
<p><strong>First, <a href="https://docs.anaconda.com/anaconda/install/">install Anaconda following this tutorial</a></strong></p>
Expand Down Expand Up @@ -157,6 +159,11 @@ <h2 id="examples">Examples</h2>
<strong>Google Colab while using a NVIDIA GPU</strong> is <a href="https://colab.research.google.com/drive/1xE6Pm1u-XoSWV8a3oYpixUFj64FIDtl0?usp=sharing">available here</a></li>
</ul>
<hr />
<h2 id="liana-tensor-cell2cell">LIANA &amp; Tensor-cell2cell</h2>
<p>Quickstart and extended tutorials are available for <a href="https://ccc-protocols.readthedocs.io/">using Tensor-cell2cell in combination with LIANA</a></p>
<p>These tutorials include the use of multiple LR-based tools running on LIANA, different databases of ligand-receptor interactions,
downstream analyses, and the use of spatial transcriptomics.</p>
<hr />
<h2 id="common-issues">Common issues</h2>
<ul>
<li>When running Tensor-cell2cell (<code>InteractionTensor.compute_tensor_factorization()</code> or <code>InteractionTensor.elbow_rank_selection()</code>), a common error is
Expand Down Expand Up @@ -187,6 +194,14 @@ <h2 id="citation">Citation</h2>
<em>Nat. Commun.</em> <strong>13</strong>, 3665 (2022). <strong>DOI: 10.1038/s41467-022-31369-2</strong></li>
</ul>
</li>
<li>
<p><strong>LIANA &amp; Tensor-cell2cell tutorials</strong> should be cited unsing this pre-print article:</p>
<ul>
<li>Baghdassarian H., Dimitrov D., Armingol E., Saez-Rodriguez J., Lewis N.E.
<a href="https://doi.org/10.1101/2023.04.28.538731">Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples</a>
<em>bioRxiv</em> (2023) <strong>DOI: 10.1101/2023.04.28.538731</strong></li>
</ul>
</li>
</ul>

</div>
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14 changes: 13 additions & 1 deletion index.md
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[pypi]: https://pypi.org/project/cell2cell/

## Getting started
Please refer to the [cell2cell website](https://earmingol.github.io/cell2cell/),
Please refer to the [cell2cell website](https://cell2cell.readthedocs.org),
which includes tutorials and documentation


Expand Down Expand Up @@ -68,6 +68,13 @@ body of *C. elegans*** is [available here](https://github.com/LewisLabUCSD/Celeg
**Google Colab while using a NVIDIA GPU** is [available here](https://colab.research.google.com/drive/1xE6Pm1u-XoSWV8a3oYpixUFj64FIDtl0?usp=sharing)


---
## LIANA & Tensor-cell2cell

Quickstart and extended tutorials are available for [using Tensor-cell2cell in combination with LIANA](https://ccc-protocols.readthedocs.io/)

These tutorials include the use of multiple LR-based tools running on LIANA, different databases of ligand-receptor interactions,
downstream analyses, and the use of spatial transcriptomics.
---
## Common issues
- When running Tensor-cell2cell (```InteractionTensor.compute_tensor_factorization()``` or ```InteractionTensor.elbow_rank_selection()```), a common error is
Expand All @@ -90,3 +97,8 @@ associated with Memory. This may happen when the tensor is big enough to make th
- Armingol E., Baghdassarian H., Martino C., Perez-Lopez A., Aamodt C., Knight R., Lewis N.E.
[Context-aware deconvolution of cell-cell communication with Tensor-cell2cell](https://doi.org/10.1038/s41467-022-31369-2)
*Nat. Commun.* **13**, 3665 (2022). **DOI: 10.1038/s41467-022-31369-2**

- **LIANA & Tensor-cell2cell tutorials** should be cited unsing this pre-print article:
- Baghdassarian H., Dimitrov D., Armingol E., Saez-Rodriguez J., Lewis N.E.
[Combining LIANA and Tensor-cell2cell to decipher cell-cell communication across multiple samples](https://doi.org/10.1101/2023.04.28.538731)
*bioRxiv* (2023) **DOI: 10.1101/2023.04.28.538731**
7 changes: 7 additions & 0 deletions requirements.in
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mkdocs
mkdocstrings[python]
markdown-include
mkdocs-autorefs
mkdocs-material
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mkdocs-jupyter
270 changes: 270 additions & 0 deletions requirements.txt
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# The following packages are considered to be unsafe in a requirements file:
# setuptools
2 changes: 1 addition & 1 deletion search/search_index.json

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