[![Project generated with PyScaffold](https://img.shields.io/badge/-PyScaffold-005CA0?logo=pyscaffold)](https://pyscaffold.org/)
[![PyPI-Server](https://img.shields.io/pypi/v/SingleCellExperiment.svg)](https://pypi.org/project/SingleCellExperiment/)
![Unit tests](https://github.com/BiocPy/SingleCellExperiment/actions/workflows/pypi-test.yml/badge.svg)

# SingleCellExperiment

Container class to represent single-cell experiments; follows Bioconductor's [SingleCellExperiment](https://bioconductor.org/packages/release/bioc/html/SingleCellExperiment.html).


## Install

Package is published to [PyPI](https://pypi.org/project/singlecellexperiment/)

```shell
pip install singlecellexperiment
```

## Usage

Readers are available to read AnnData, H5AD or 10x (MTX, H5) V3 formats as `SingleCellExperiment` objects.

```python
import singlecellexperiment

sce = singlecellexperiment.read_h5ad("tests/data/adata.h5ad")
```

    ## output
    class: SingleCellExperiment
    dimensions: (20, 30)
    assays(3): ['array', 'sparse', 'X']
    row_data columns(5): ['var_cat', 'cat_ordered', 'int64', 'float64', 'uint8']
    row_names(0):
    column_data columns(5): ['obs_cat', 'cat_ordered', 'int64', 'float64', 'uint8']
    column_names(0):
    main_experiment_name:
    reduced_dims(0): []
    alternative_experiments(0): []
    row_pairs(0): []
    column_pairs(0): []
    metadata(2): O_recarray nested

***OR construct one from scratch***

```python
from singlecellexperiment import SingleCellExperiment

tse = SingleCellExperiment(
    assays={"counts": counts}, row_data=df_gr, col_data=col_data,
    reduced_dims={"tsne": ..., "umap": ...}, alternative_experiments={"atac": ...}
)
```

Since `SingleCellExperiment` extends `SummarizedExperiment`, most methods especially slicing and accessors are applicable here. Checkout the [documentation](https://biocpy.github.io/SingleCellExperiment/) for more info.

<!-- pyscaffold-notes -->

## Note

This project has been set up using PyScaffold 4.5. For details and usage
information on PyScaffold see https://pyscaffold.org/.