Collections / geo-gse305111

geo-gse305111

Datasets3
Size~1.7 MB
TechnologyStereo-seq
Samplepig · skin of body
KindOther
Flag a data issue
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse305111")
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/")
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-gse305111")
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()]
Install (Python 3.12+) Docs →
Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse305111 --dest data/
Install (Python 3.12+) Docs →

Licenses: 3 NCBI GEO policy

Member datasets · 3
Open in Vitessce
Stereo-seq
Pig skin of body
GSM9162384
pig skin of body 350 KB 6,054 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismpig
Tissueskin of body
Size350 KB
Obs6,054
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Pig skin of body
GSM9162385
pig skin of body 654 KB 13,609 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismpig
Tissueskin of body
Size654 KB
Obs13,609
bronze NCBI GEO policy Open in Vitessce
Open in Vitessce
Stereo-seq
Pig skin of body
GSM9162386
pig skin of body 677 KB 13,986 obs bronze NCBI GEO policy
TechnologyStereo-seq
Organismpig
Tissueskin of body
Size677 KB
Obs13,986
bronze NCBI GEO policy Open in Vitessce