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Hello Tangram developers,
I'd like to ask a question that might help me clarify whether Tangram is a good choice for my large visium dataset.
So, it seems to me that Tangram works best when bot…
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Hello, thank you for developing this excellent tool.
I want to use the recently published Allen Brain Atlas MERFISH data as my reference, as it is of the single-cell resolution.
My data that I want …
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Right now `spatialLIBD` is built upon the `SpatialExperiment` container class. There is also https://bioconductor.org/packages/SpatialFeatureExperiment/ that can support non-Visium spatially-resolved …
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Traceback (most recent call last):
File "F:/SiGra-main/SiGra_model/train.py", line 32, in
train_10x(opt)
File "F:\SiGra-main\SiGra_model\train_visium.py", line 237, in train_10x
ARI =…
12hsk updated
4 months ago
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I am trying to merge 2 Seurat objects containing data loaded from VisiumHD technology:
```
> x1 x2 merge(x1, x2)
Warning: Some cell names are duplicated across objects provided. Renaming to enf…
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Hello again!
I've been trying out the bivariate approach with the Visium HD data, and I've been testing some of the parameters, mainly bandwidth and max_neighbours:
```
li.ut.spatial_neighbors…
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Hi, I had some questions about the cluster annotation after cell segmentation
I tried to map the single-cell data to Visium and got the probability of the spatial location of cell group ExcNeurons3…
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Thank you very much for `bin2cell`.
@ktpolanski is `b2c.view_labels()` in 0.3.2 the unformalized custom function @nadavyayon referred to and was using at 18 minutes and 35 seconds (18:35) in the Se…
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I just recently updated to Seurat v5. I was attempting to run FindSpatiallyVariableFeatures() on a (single) merged object from two Visium slices similarly as explained by tingchiafelix in issue https:…
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Hi, I am trying to use this with a non-10X count matrix and 10X Visium barcodes. How can I generate the SingleCellExperiment object using my count matrix (standard format) and the Visium barcodes + co…