Cellarium Cell Annotation Service client tool
Project description
Cellarium Cell Annotation Service (CAS) Client
This codebase contains the Python client library for using Cellarium Cell Annotation Service (CAS).
Installation
$ pip install cellarium-cas
Usage
To use Cellarium CAS, create a client instance with your API token:
from cellarium.cas import CASClient
api_token = "a_very_long_string_with_some_symbols"
cas = CASClient(
api_token=api_token,
api_url="<optional url to connect to a non-standard CAS server>"
)
Annotation
You can annotate 10x Cell Ranger h5 matrices from local disk:
response = cas.annotate_10x_h5_file(filepath="your_path_to_local_h5_file.h5")
or an anndata file from local disk:
response = cas.annotate_anndata_file(filepath="your_path_to_local_h5_file.h5ad")
or a previously loaded (unnormalized) anndata object:
import anndata
adata = anndata.read("you_anndata_file.h5ad")
response = cas.annotate_anndata(adata)
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