Usage

API Token

You need to request an API token before you can use it. Please contact our team by mehrtash@broadinstitute.org if you’re interested in our tool and we will create an API token for your needs.

Initialization

Create a CASClient instance with your API token:

from cellarium.cas import CASClient

api_token = "api_token_string_goes_here"
cas = CASClient(api_token=api_token)

Annotation

10x Cell Ranger h5 matrices

You can annotate 10x Cell Ranger h5 matrices from the local disk:

response = cas.annotate_10x_h5_file(filepath="your_path_to_local_h5_file.h5")

Anndata File from the disk

response = cas.annotate_anndata_file(filepath="your_path_to_local_h5_file.h5ad")

Anndata File instance

import anndata


adata = anndata.read("you_anndata_file.h5ad")
response = cas.annotate_anndata(adata)