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)
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
cellarium-cas-1.4.6.tar.gz
(118.9 kB
view hashes)
Built Distribution
cellarium_cas-1.4.6-py3-none-any.whl
(126.4 kB
view hashes)
Close
Hashes for cellarium_cas-1.4.6-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | d5fcd60a9244a21799dec25cb0ee3d0fd0ff6bd3f5a48e819935808430dc564b |
|
MD5 | c3545d2d627defcb0abd40b8ee9e777f |
|
BLAKE2b-256 | b56e51e736a2cf2cff16642d996842c70c53399091839ac87e87e8a21513a248 |