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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/js2264/OHCA
Confirm the following by editing each…
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I have a SpatialExperiment (similar to SingleCellExperiment) object and a Seurat object both containing the same 10x Visium experiment. The experiment objects contains 4 images and associated assay. I…
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### This is my SpatialExperiment object:
```
spatial_data
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Hi
I am on a mac with OSX 13 and with R4.2.2 and I get the following error:
` library(imcRtools)
Loading required package: SpatialExperiment
Error: package or namespace load failed for ‘Spatial…
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Hi,
I am trying to run spotlight on a visium mouse brain dataset but the R studio session keeps crashing. Here is the code:
library(ggplot2)
library(SPOTlight)
library(SingleCellExperiment)…
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Hi Brendan,
I hope this inquiry finds you well, and thank you very much for kindly answering my questions. :)
I'm also trying to validate my cell type deconvolution results by integrating 3 Visi…
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Can I run compare_seurat (or compare_sce) on a Seurat object that contains a 10x Visium dataset for pathway analysis? Within the Seurat object is 4 microscope images with accompanying assays. I also h…
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Thank you for this amazing tool! I have tried it out on my data and SPOTlight function worked beautifully on individual samples, however, I would like to train a model on one sample and use it for oth…
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There is a corner case for `nnSVG` where the LR test would be wrong. The corner case is happens when testing the spatial effect with an intercept-less covariate model (see code example below). This bu…
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The function does not handle the edge case if one of the CellTypes/labels has only one cell present in an ROI with no neighbors in expansion threshold. Throws an error in:
dat_stat[is.na(dat_baseli…