cellarium-cas 0.0.3

Cellarium Cell Annotation Service client tool

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)