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feiyoung / PRECAST

an efficient data integration method for multiple spatial transcriptomics data with non- cluster-relevant effects such as the complex batch effects.
GNU General Public License v3.0
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Run PRECAST with SpatialExperiment #1

Closed boyiguo1 closed 2 years ago

boyiguo1 commented 2 years ago

Because the PRECAST pipeline is based on Seurat, which creates difficulty for bio conductor users who's familiar with spatialExperiment.

I wrote these wrapper functions to convert a spatialExperiment (possibly multiple samples in the same object) to seuraList for anyone who wants to use. Please find them in https://github.com/feiyoung/PRECAST_Analysis/issues/1#issuecomment-1261295891.

feiyoung commented 2 years ago

Hi Boyi. Thank you for your provided wrapper function for spatialExperiment and valuable feedback. We will optimize the package to make it easy-used for users, such as adding the inerface for spatialExperiment and SingleCellExperiment, and writing more detailed vigenettes. Thank you again!

boyiguo1 commented 2 years ago

Haha, just to be clear, I didn't mean to push you to do anything. I appreciate you are working on such a valuable method/tool.