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JinmiaoChenLab / GraphST

GNU Affero General Public License v3.0
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Can GraphST be applied for merfish? #28

Open Byronxy opened 5 months ago

Byronxy commented 5 months ago

Dear developers, Thanks for developing this great tool. Can I use this tool for processing merfish data and integrate scRNAseq data with merfish?

Rafael-Silva-Oliveira commented 5 months ago

From their paper "We designed GraphST to be user-friendly and capable of processing data acquired from different experimental platforms. GraphST has been validated on 10x Visium, Slide-seqV2, and Stereo-seq data, and we plan to extend it to other ST platforms, such as MERFISH and Nanostring CosMx SMI."

So I don't think so. Plus, the largest dataset they've tested had around 100k spots and the new VisiumHD at 8 micron resolution bin can have over 500k spots. So my guess is that GraphST is not yet capable of handling very big/granular datasets unfortunately.