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Chunfu-Shawn / STellaris-Analysis-Pipeline

STellaris Pipeline
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Create a Shiny package for handling spatial transcriptomics data #2

Open howtofindme opened 3 weeks ago

howtofindme commented 3 weeks ago

Hi, Wonderful job!

I have searched through many articles and am looking for a Shiny app that can handle spatial transcriptomics data in a similar manner to how Shinycell handles single-cell transcriptomics data.

However, currently, there is no R package available that fulfills this requirement.

However, I noticed that your home page can visualize the spatial data. many researchers are only familiar with using the Seurat package for spatial transcriptomics data analysis, would you be able to create an interface for the Seurat package so that Visium Seurat objects can be used to create Shiny apps like your homepage? With the increasing depth of research in spatial transcriptomics, I believe this feature would greatly advance the field. Looking forward to your response. Best, Young

Chunfu-Shawn commented 3 weeks ago

Hello Young, Thanks for your praise. Our web visualizes the spatial trans data using a tool (https://github.com/Chunfu-Shawn/Spatial-Trans-Visual-Tool), which was adjusted from Cirrocumulus. This tool was developed to visualize ST data under serverless, and anyone can use it after processing the ST data (.h5ad) to .jsonl data. Details are shown in the repository. Moreover, i reviewed a recent unpublished paper reporting a visuallization package for Seurat data, which utilizes a Shiny application to generates an interactive and shareable interface via the web. I hope it would be published before long and resolve your issue.