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Hi,
When I ran inferIntrScore() and inferSignif() on my own dataset, it gave following messages:
```
== Calculating diffusible ligand-receptor scores ==
Computing LR-scores using diff_dep da…
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Hi,
Thanks for maintaining SPATA2!
I have a seurat object after QC and SCT normalized, which was used for spata trajectory analysis. I am confused by the structure of spata2 object.
Q1. What infor…
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Hi,
In the paper (SpatialDWLS: accurate deconvolution of spatial transcriptomic data), in figure 2C there was a bar plot of the different composition of deconvoluted cell types generated - this gr…
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- [x] Introduction - scope 0.5-1 page
- look into reviews
- broad overview into the field
- mention nature methods "method of the year 2020"
- define axis: targeted/high-resolution vs unbiased…
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Hello,
Thank you for the work on the STAMarker tool. I am interested in using STAMarker to analyze my own spatial data. However, while following the tutorial provided in "Mouse-cerebellum.ipynb," I h…
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Hi @gcyuan @bernard2012 @wwang-chcn @RubD @pacificma , thanks for your contribution to Giotto and Binspect! I used Binspect-rank to analyze the spatially variable genes in my spatial data (~40000 cell…
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### Task motivation
Spatially resolved transcriptomics offers unprecedented insight by enabling the profiling of gene expression within the intact spatial context of cells, effectively adding a new a…
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Hello, can you provide the data for analysis in visium_human_dorsolateral_prefrontal_Cortex.r?
I can get the raw data, but I'm not sure what goes from the raw data to the data for your analysis.
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- download a data of choice from 10x genomics (you can browse them [here](https://support.10xgenomics.com/spatial-gene-expression/datasets))
- find a way to load them in R with this
- otherwise, d…
giovp updated
3 years ago
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Dear Brendan,
I am using stdeconvolve with an 8-sample visium integrated seurat object. All samples were individually normalized with seurat's sctransform algorithm before anchor-based integration …