# Documentation

Harreman (Basque for "receive" and "give") is a Python package for metabolic cell-cell communication inference in spatial transcriptomics data. Harreman is interoperable with [AnnData](https://anndata.readthedocs.io/en/latest/) objects and it is developed and maintained by the [Yosef Lab](https://www.weizmann.ac.il/immunology/yosef/) at the Weizmann Institute of Science.

![overview](figs/Harreman_pipeline.png)

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

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

Check out the installation guide.
:::

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

The user guide provides mathematical descriptions of
the statistical models implemented in Harreman and connects the math
with the code.
:::

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

Learn by following example applications of Harreman.
:::

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

The API reference contains a detailed description of
the Harreman API.
:::

:::{grid-item-card} Release Notes {octicon}`tag;1em;`
:link: release_notes/index
:link-type: doc

Follow the latest changes to Harreman.
:::

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

Checkout our GitHub for the latest developments.
:::
::::

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

installation
user_guide/index
tutorials/index
api/index
release_notes/index
references.md
GitHub <https://github.com/YosefLab/Harreman>