Spatial transcriptomics was performed on human hepatoblastomas to determine features associated with histologic heterogeneity.
from sddb import Catalog
cohort = Catalog().collection("geo-gse249965")
cohort.members # the 3 datasets as a table
print(cohort.licenses()) # check the terms before you download
sdatas = cohort.to_dict() # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse249965")
coll.ordered_artifacts.to_dataframe() # the 3 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse249965 --dest data/Licenses: 3 NCBI GEO policy
@article{Wu_2024,
title = {A developmental biliary lineage program cooperates with Wnt activation to promote cell proliferation in hepatoblastoma},
volume = {15},
ISSN = {2041-1723},
url = {http://dx.doi.org/10.1038/s41467-024-53802-4},
DOI = {10.1038/s41467-024-53802-4},
number = {1},
journal = {Nature Communications},
publisher = {Springer Science and Business Media LLC},
author = {Wu, Peng V. and Fish, Matt and Hazard, Florette K. and Zhu, Chunfang and Vennam, Sujay and Walton, Hannah and Wagh, Dhananjay and Coller, John and Przybyl, Joanna and Morri, Maurizio and Neff, Norma and West, Robert B. and Nusse, Roel},
year = {2024},
month = Nov
}