Metadata-Version: 2.1
Name: pyBCS-bioturing
Version: 0.4.1
Summary: Create BioTuring Compressed Study (bcs) file
Home-page: https://www.bioturing.com
Author: BioTuring
Author-email: support@bioturing.com
License: UNKNOWN
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.6
Description-Content-Type: text/markdown
Requires-Dist: scanpy (>=1.6.0)
Requires-Dist: anndata (>=0.7.5)
Requires-Dist: loompy (>=3.0.6)

# pyBCS

This is a python library to create a BioTuring Compressed Study (`bcs`) file from an AnnData (scanpy) object.

`bcs` files can be imported directly into [BBrowser](https://bioturing.com/bbrowser), a software for single-cell data.

Visit our [github](https://github.com/bioturing/pyBCS) for more detail.

## Example

### Scanpy

```python
from pyBCS import scanpy2bcs
scanpy2bcs.format_data("/mnt/example/data.h5ad", "/mnt/example/data.bcs",
                        input_format="h5ad", graph_based="louvain")
```


### SPRING

```python
from pyBCS import scanpy2bcs
scanpy2bcs.format_data("/mnt/example/spring_study", "/mnt/example/data.bcs",
                        input_format="spring",
                        graph_based="louvain")
```

### Loom

```python
from pyBCS import scanpy2bcs
scanpy2bcs.format_data("/mnt/example/data.loom", "/mnt/example/data.bcs",
                        input_format="loom",
                        barcode_name="CellID",
                        feature_name="Gene",
                        dimred_keys={"tsne":["tsne1", "tsne2"]})
```

### Abloom

```python
from pyBCS import scanpy2bcs
scanpy2bcs.format_data("/mnt/example/data.loom", "/mnt/example/data.bcs",
                        input_format="abloom",
                        barcode_name="observation_id",
                        feature_name="accession_id",
                        graph_based="cluster")
```


