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Hi,
Thank you very much for developing such an excellent tool for cell communication, especially for the spatial transcriptome.
I am recently using cellchat to analyze the interaction of sp…
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Thanks for the wonderful tool
I was wondering whether it would be possible to load visium HD data with the current version
and go on to the downstream analysis
if not, would there be any plan …
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Hello, I am trying to load visium HD data using the following command:
Load10X_Spatial(data.dir = localdir, filename="filtered_feature_bc_matrix.h5")
However, my r session is killed. The size of…
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Hi all,
I try to follow the tutorial on cell annotation for visium data [https://satijalab.org/seurat/articles/spatial_vignette](url). However, I got zero score for many cell types should have in b…
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Hello, thank you for developing this great and easy to use tool. Have you got any recommendations on using it for non sequencing-based transcriptomic methods e.g. 10X Visium? What are the implications…
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Hello SCIMAP developers,
I wanted to know if it is possible to use either MERFISH or Visium data with this tool, and how would one go about doing so. Because, I keep encountering an error with rega…
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Hi! Thanks for the great tool! Could GeneNMF be applied to 10x visium data ?
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Hi,
I am currently trying to combine my processed Visium and scRNAseq data using the multimodal run. Following the tutorial I was able to process the data and was able to see the combine feature (G…
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asSPATA2(sp, sample_name="ch", spatial_method="Visium", image_name="s1")
sp is an seurat object with Visium spatial method and is not CytAssist, but asSPATA2 gives the below error.
Error in (func…
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Hi, I get an error when trying to read in a Visium HD dataset with the visium_hd reader of v0.1.5. The same code works perfectly fine with v0.1.4.
```
from spatialdata_io import visium_hd
sdata …