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YangLabHKUST / SpatialScope

A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models
https://spatialscope-tutorial.readthedocs.io/en/latest/
GNU General Public License v3.0
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Visium multiple slides #1

Closed spatialbiology1 closed 1 year ago

spatialbiology1 commented 1 year ago

Thanks so much for the great tool! Can we integrate multiple slides from primary and metastatic samples.? I am analyzing N= 30 samples from primary tumor, lymph nodes and lung metastasis. Many thanks Zinn

JiaShun-Xiao commented 1 year ago

Hi, Zinn,

It is feasible to apply our tool to multiple samples by analyzing one ST sample at a time. In this way, we will separately account for batch effects between the scRNA-seq reference and each ST sample, making cell type identification results immune to batch effects (both among ST samples and between ST and scRNA-seq ref) and consistent across multiple samples.

best wishes, Jiashun