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kaishumason / NicheDE

NicheDE is a method that detects context dependent changes in gene expression in spatial transcriptomic data.
https://kaishumason.github.io/NicheDE/
MIT License
14 stars 1 forks source link

Function to creates the niche-DE object from a seurat 10X Xenium object #4

Open nilesh-iiita opened 7 months ago

nilesh-iiita commented 7 months ago

Description:

The current implementation of the CreateNicheDEObjectFromSeurat lacks support for converting the Seurat 10X Xenium object to the niche-DE format. As a result, users are unable to seamlessly transition data from Seurat 10X Xenium to niche-DE for further analysis.

Expected Behavior:

Users should be able to utilize CreateNicheDEObjectFromSeurat to successfully convert Seurat 10X Xenium objects into the niche-DE format, enabling smooth integration and analysis of data across platforms.

Steps to Reproduce:

  1. Attempt to convert a Seurat 10X Xenium object to niche-DE using CreateNicheDEObjectFromSeurat.
  2. Notice the absence of support for this conversion.
  3. Encounter difficulty in transitioning data between Seurat 10X Xenium and niche-DE platforms.

@lianov

kaishumason commented 7 months ago

I see, thank you for pointing this out! I will look into this and let you know when it is resolved.

kaishumason commented 1 month ago

Hi Nilesh, The issue should be fixed now.