# Documentation

`scvi-tools` (single-cell variational inference tools) is a package for end-to-end analysis of
single-cell omics data primarily developed and maintained by the
[Yosef Lab](https://www.weizmann.ac.il/immunology/yosef/) at the Weizmann Institute of Science.
`scvi-tools` has two components:

-   Interface for easy use of a range of probabilistic models for single-cell omics (e.g., scVI, scANVI, totalVI).
-   Tools to build new probabilistic models, which are powered by PyTorch, PyTorch Lightning, and Pyro.

If you find a model useful for your research, please consider citing the [scvi-tools manuscript](http://dx.doi.org/10.1038/s41587-021-01206-w) as well as the publication describing the model, which can be found in the corresponding documentation.

[//]: # (numfocus-fiscal-sponsor-attribution)

scvi-tools is part of the scverse® project ([website](https://scverse.org), [governance](https://scverse.org/about/roles)) and is fiscally sponsored by [NumFOCUS](https://numfocus.org/).
If you like scverse® and want to support our mission, please consider making a tax-deductible [donation](https://numfocus.org/donate-to-scverse) to help the project pay for developer time, professional services, travel, workshops, and a variety of other needs.

<div align="center">
<a href="https://numfocus.org/project/scverse">
  <img
    src="https://raw.githubusercontent.com/numfocus/templates/master/images/numfocus-logo.png"
    width="200"
  >
</a>
</div>

::::{grid} 1 2 3 3
:gutter: 2

:::{grid-item-card} Installation {octicon}`plug;1em;`
:link: installation
:link-type: doc

New to _scvi-tools_? Check out the installation guide.
:::

:::{grid-item-card} User guide {octicon}`info;1em;`
:link: user_guide/index
:link-type: doc

The user guide provides distilled mathematical descriptions of
the models implemented in scvi-tools and connects the math
with the code.
:::

:::{grid-item-card} API reference {octicon}`book;1em;`
:link: api/index
:link-type: doc

The API reference contains a detailed description of
the scvi-tools API.
:::

:::{grid-item-card} Tutorials {octicon}`play;1em;`
:link: tutorials/index
:link-type: doc

The tutorials walk you through real-world applications of scvi-tools models.
Developer tutorials help you build new probabilistic models.
:::

:::{grid-item-card} Discussion {octicon}`megaphone;1em;`
:link: https://discourse.scverse.org/

Need help? Reach out on our forum to get your questions answered!
:::

:::{grid-item-card} GitHub {octicon}`mark-github;1em;`
:link: https://github.com/scverse/scvi-tools

Find a bug? Interested in improving scvi-tools? Check out our GitHub for the latest developments.
:::
::::

```{toctree}
:hidden: true
:maxdepth: 2
:titlesonly: true

installation
tutorials/index
user_guide/index
api/index
developer/index
faq
changelog.md
references
Discussion <https://discourse.scvi-tools.org>
GitHub <https://github.com/scverse/scvi-tools>
Model hub <https://huggingface.co/scvi-tools>
```