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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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Hello!
I want to open discussion about adding a support for [TreeSummarizedExperiment](https://bioconductor.org/packages/release/bioc/vignettes/TreeSummarizedExperiment/inst/doc/Introduction_to_tre…
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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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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
8 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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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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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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Please briefly describe your problem and what output you expect. If you have a question, please don't use this form.
Instead, ask on our [Community Forum](https://github.com/icbi-lab/immunedeconv/dis…
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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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Hi there, just wanted to file an issue on a small roadblock I ran into. The dataset (HEST [1]) I'm working with has some downscaled images with the extension `.jpeg` which trips the validity check [he…