Collections / geo-gse317062

geo-gse317062

Datasets4
Size~392 MB
AssayStereo-seq
Samplerat · ileum
KindOther
Flag a data issue
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse317062")
cohort.members        # the 4 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/")
Install (Python 3.12+) Docs →
Python · lamindb

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-gse317062")
coll.ordered_artifacts.to_dataframe()   # the 4 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse317062 --dest data/
Install (Python 3.12+) Docs →

Licenses: 4 NCBI GEO policy

Member datasets · 4
Open in Vitessce
Stereo-seq
Rat ileum
GSM9464516
rat ileum 89.9 MB 25,224 cells bronze NCBI GEO policy
TechnologyStereo-seq
Organismrat
Tissueileum
Size89.9 MB
Cells25,224
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Rat ileum
GSM9464517
rat ileum 70.5 MB 15,207 cells bronze NCBI GEO policy
TechnologyStereo-seq
Organismrat
Tissueileum
Size70.5 MB
Cells15,207
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Rat ileum
GSM9464519
rat ileum acute pancreatitis 118 MB 22,966 cells bronze NCBI GEO policy
TechnologyStereo-seq
Organismrat
Tissueileum
Conditionacute pancreatitis
Size118 MB
Cells22,966
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Rat ileum
GSM9464518
rat ileum acute pancreatitis 113 MB 23,840 cells bronze NCBI GEO policy
TechnologyStereo-seq
Organismrat
Tissueileum
Conditionacute pancreatitis
Size113 MB
Cells23,840
bronze NCBI GEO policy Open in Vitessce