# SingleCellExperiment

This package provides container class to represent single-cell experimental data as 2-dimensional matrices. In these matrices, the rows typically denote features or genomic regions of interest, while columns represent cells. In addition, a `SingleCellExperiment` (SCE) object may contain low-dimensionality embeddings, alternative experiments performed on same sample or set of cells. Follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).


## Install

To get started, install the package from [PyPI](https://pypi.org/project/singlecellexperiment/)

```bash
pip install singlecellexperiment
```

## Contents

```{toctree}
:maxdepth: 2

Overview <tutorial>
Module Reference <api/modules>
Contributions & Help <contributing>
License <license>
Authors <authors>
Changelog <changelog>
```


## Indices and tables

- {ref}`genindex`
- {ref}`modindex`
- {ref}`search`

[Sphinx]: http://www.sphinx-doc.org/
[Markdown]: https://daringfireball.net/projects/markdown/
[reStructuredText]: http://www.sphinx-doc.org/en/master/usage/restructuredtext/basics.html
[MyST]: https://myst-parser.readthedocs.io/en/latest/