Edward Zhao

Thanks both for noticing this problem. The admin who manages the cloud storage accidentally changed the permissions for these files. It should be fixed as of ~30 minutes ago. Can...

You might be using a older version of R/Bioconductor. Can you check if the fix in #51 works?

I'm not sure I understand the question. Are you trying to run BayesSpace on data that isn't from Visium?

Thanks for giving our tool a try. I think the results you are describing are not unusual. The main source of the discrepancy probably arises from the difference in neighborhood...

Sorry for the delayed response. With Visium data, we use the image coordinates to calculate distance instead of the array coordinates. These should be a part of the SpaceRanger output...

Sorry not sure I understand. `getRDS()` provides a SingleCellExperiment object. You can create your own Seurat object using the [`CreateSeuratObject()`](https://www.rdocumentation.org/packages/Seurat/versions/3.0.1/topics/CreateSeuratObject) function.

Please try the solution from #48. Hope this helps.

Sorry for the delayed response. I think the issue is because you need to offset the `row` and/or `col` values first. The first code chunk under the "Clustering" header in...

@msto do you recall why we used different functions for finding neighbors? Was it due to the non-integer coordinates for subspots?

@lcolladotor I'll look into this. But I think you might run into more memory issues (not to mention compute time) doing the enhancement on this large dataset. We'll try to...