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Hello, I am now using snRNAseq and scATACseq to reproduce the development trajactories reported in your great paper. But I encountered a problem that while I utilized the h5 formatted data output by c…
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Good day,
I recently noticed when toggling to subset a specific subcluster in the violin plot function on the shiny app that some of the expression values are negative. I'm not sure why this is th…
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Hi @yunguan-wang,
I noticed in the manuscript it noted that parallel processing actually resulted in slower jobs (presumably implemented in R), but spacia.py has a worker pool. It appears to batch…
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Hi,
thanks for this very useful tool.
I am trying to run lemur on my dataset (snRNAseq of 10 tumor samples before and after chemotherapy) but when I run the command:
`fit Storing 50% of the data (…
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Hi Sam,
I am trying to use Iterate_FeaturePlot_scCustom to plot my top marker genes calculated using your tools, but I get an error. I have confirmed that my Seurat object and top_markers are of th…
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Hi team,
Are there any plans to create a mouse benign pancreas or malignant pancreas profile that can be used for any cosmx experiments run on pancreas cancer mouse models?
Best,
Alex
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**Description of the task:**
For datasets ingested before the ontology labels were updated, we need to update the 10x library preparation method (before: 10x 3' v2 sequencing, now only 10x 3' v2)
Li…
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Dear developers,
thanks for creating this great package and the comprehensive, easy-to-follow vignettes! I am fairly new to bioinformatics and single cell analyses and want to use CellChat for a n…
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Hi,
Is it possible to run gpsFISH without spatial count and spatial cluster datasets (or can it run with spatial count and cluster datasets provided in the tutorial)? I am working with the datasets…
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Hi, I am trying to use my matched snRNAseq and CosMx data to predict cell types for the CosMx data from the snRNAseq. I generally have the code together (See #8660 for a related issue), but I want to …