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Thanks for creating and maintaining the package.
I'm experimenting the `SpatialExperiment::read10xVisium`to import the Visium HD data via https://www.10xgenomics.com/datasets/visium-hd-cytassist-ge…
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Hello,
I ran `BayesSpace` with k = 28 for ~113,000 spots. I've noticed that I only get 26 clusters because clusters 18 and 21 are missing. Is this to be expected? Is it possible, `BayesSpace` is m…
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Hello,
I ran into a case where I found it useful to apply rotations, reflections, and translations to the entire `SpatialExperiment` object. So far, I just wrote code to adjust the `spatialCoords` …
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Hi,
After updating the release version of the package to 1.6.1, the function `toSpatialFeatureExperiment()` stopped working. Here is a minimal reproducing example:
```r
library(SpatialExperimen…
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Hello,
I have been getting this memory issue with minDistToCells. Each image is 100k-400k cells and there are 800k cells in total in the dataset. I have a suspicion that this may be some sort of v…
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Hi! I commented on an enhancement in issues as I originally thought it might be an issue of my spatial experiment, however I'm wondering if this is a separate issue.
I tried to convert the spe int…
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Hi,
I've been trying to replicate my previous scripts and data pipeline from earlier versions of Seurat. I'm trying to recluster the clusters I found earlier. However, I'm encountering a particular…
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Hi,
While using `BayesSpace` version 1.4.1, I'm running `spatialEnhance()` on a dataset with the following dimensions:
```R
> dim(spe)
[1] 27853 38115
```
with it, I get the following erro…
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/ZheFrench/BulkSignalR
Confirm the following by ed…
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hi Nick,
thanks for the great tool!
Below is the code that I use to process TRUST4 output and combineTCR; it had worked perfectly fine a couple weeks ago, but today I was rerunning the code and …