The simplest way to get a list of collections is to use the :meth:`nbiatoolkit.NBIAClient.getCollections` method. This method returns a list of all collections available in the NBIA database.
The method has the following signature:
.. automethod:: nbiatoolkit.NBIAClient.getCollections
Passing no parameters to the method will return a list of all collections available in the NBIA database. Passing a prefix parameter will return a list of collections that match the prefix.
.. tabs::
.. tab:: Python
.. exec_code::
# --- hide: start ---
from nbiatoolkit import NBIAClient
from pprint import pprint as print
# --- hide: stop ---
client = NBIAClient(return_type = "dataframe")
collections_df = client.getCollections(prefix='TCGA')
print(f"The number of available collections is {len(collections_df)}")
print(collections_df)
.. automethod:: nbiatoolkit.NBIAClient.getCollectionDescriptions
.. tabs::
.. tab:: Python
.. exec_code::
# --- hide: start ---
from nbiatoolkit import NBIAClient
from pprint import pprint as print
# --- hide: stop ---
with NBIAClient() as client:
desc = client.getCollectionDescriptions(collectionName = "TCGA-BLCA")[0]
print(desc['Description'])
print(desc['DescriptionURI'])
print(desc['LastUpdated'])
.. automethod:: nbiatoolkit.NBIAClient.getCollectionPatientCount
.. tabs::
.. tab:: Python
.. exec_code::
# --- hide: start ---
from nbiatoolkit import NBIAClient
# --- hide: stop ---
with NBIAClient() as client:
counts_df = client.getCollectionPatientCount(
prefix = "TCGA",
return_type="dataframe"
)
print(counts_df)