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Can iSEE support Spatial transcriptomics data that is contained within a SPE (SpatialExperiment) object? I have 10x Visium data in an SPE and tried running ```iSEE(SPE)``` which opened a shiny app wit…
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Good afternoon SpatialExperiment team,
Thank you so much for building up SpatialExperiment! As I'm transition from Seurat to SpatialExperiment I wondered f there was a way to convert Seurat objecs …
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Hi, I had a read of you preprint and think that SpaNorm looks like a great tool to test on some MERSCOPE and Xenium data I am currently analyzing. I was wondering whether the SpaNorm package can work …
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pinging interested parties @lmweber @drighelli @HelenaLC @ivirshup
Nice to meet you all! I believe with some we crossed paths in some zoom dungeons or email thread. I'd like to use this issue to k…
giovp updated
6 months ago
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In , @allyhawkins created a function `spatial_coldata_to_df()` that adds some of the data from the `spatialData` slot of a SpatialExperiment to the main `colData` contents after merging.
For scpca…
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I'm trying to annotate cell types of visium 10x data using the annotateCellTypesGSEA function. This is a minimal script to reproduce the error
```
library(STdeconvolve)
library(SpatialExperiment)
…
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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/kinnaryshah/spatialSimGP
Confirm the following by…
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Hello!
I have some seqFISH data from Spatial Genomics generated by their 'genePS' system. I was wondering if anyone had some code to import this data into a SpatialExperiment S4 R/Bioconductor clas…
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Hi, I have been using `scry::devianceResiduals()` for preprocessing and transformation in 10x Genomics Visium data, and have been running into some possible stability issues and warnings.
I am runn…
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Thanks for creating the package.
I'm experimenting with `VisiumIO` 0.99.3 to create SpatialExperiment object for Visium HD data.
The dataset that I'm experimenting right now comes from https://…