Visium Human brain
GSM8376639
human brain melanoma 13 MB 1,732 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmelanoma
Obs1,732
Magnificationother · 4.139 µm/px
bronze H&E
Collections / spatialGE is a User-Friendly Web Application that Facilitates Spatial Transcriptomics Data Analysis
spatialGE is a User-Friendly Web Application that Facilitates Spatial Transcriptomics Data Analysis
Spatial transcriptomics (ST) is a powerful tool for understanding tissue biology and disease mechanisms. However, the advanced data analysis and programming skills required can hinder researchers from realizing the full potential of ST. To address this, we developed spatialGE, a web application that simplifies the analysis of ST data. The application spatialGE provided a user-friendly interface that guides users without programming expertise through various analysis pipelines, including quality control, normalization, domain detection, phenotyping, and multiple spatial analyses. It also enabled comparative analysis among samples and supported various ST technologies. The utility of spatialGE was demonstrated through its application in studying the tumor microenvironment of two data sets: 10× Visium samples from a cohort of melanoma metastasis and NanoString CosMx fields of vision from a cohort of Merkel cell carcinoma samples. These results support the ability of spatialGE to identify spatial gene expression patterns that provide valuable insights into the tumor microenvironment and highlight its utility in democratizing ST data analysis for the wider scientific community.
Datasets2
Size~22 MB
AssayVisium
Samplehuman · brain
KindOther
Download the whole collection
Python · lamindb
import lamindb as ln
import spatialdata as sd
coll = ln.Collection.get(key="geo-gse271422")
coll.ordered_artifacts.df() # the 2 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
# …or load each straight into memory as a SpatialData object:
sdatas = {a.key: sd.read_zarr(a.cache()) for a in coll.ordered_artifacts.all()}Member datasets · 2
Visium 
Visium Human brain
GSM8376640
human brain melanoma 9.1 MB 1,302 obs bronze H&E
TechnologyVisium
Organismhuman
Tissuebrain
Conditionmelanoma
Obs1,302
bronze H&E
Cite this collection
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