pysodb is a python package that provides the interface to access the data in SODB.
- Clone the source code.
git clone https://github.com/TencentAILabHealthcare/pysodb.git
cd pysodb
- Create a conda environment and activate it.
conda env create -n pysodb --file pysodb.yml
conda activate pysodb
- Install pysodb as a dependency or third-party package with pip:
pip install .
import pysodb
sodb = pysodb.SODB() # Initialization
dataset_list = sodb.list_dataset() # Get the list of datasets
dataset_list = sodb.list_dataset_by_category() # Get the list of datasets with specific category. categories ["Spatial Transcriptomics", "Spatial Proteomics", "Spatial Metabolomics", "Spatial Genomics", "Spatial MultiOmics"]
adata = sodb.load_experiment('hunter2021spatially','sample_B') # Load a specific experiment
adataset = sodb.load_dataset('hunter2021spatially') # Load a specific dataset
Please refer to šDocumentation and Tutorials for more details.
Yuan, Z., Pan, W., Zhao, X. et al. SODB facilitates comprehensive exploration of spatial omics data. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01773-7
Spatial Omics DataBase (SODB): increasing accessibility to spatial omics data. Nat Methods (2023). https://doi.org/10.1038/s41592-023-01772-8