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11/5/19 Update. The pipeline was approved today as a standard pipeline! We will be cutting a new release to reflect the new functionality and will coordinate with folks to add the pipeline to the DCP.…
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Hi everyone,
I’m currently working on Xenium (10x Genomics) data analysis, which contains 321 targeted genes. To explore more, I would like to merge and integrate public data with my Xenium dataset…
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Error in ContaminationCorrection(nall, rownames(GCGs)) :
"counts"槽名不存在于"Assay5"类别对象中
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My seurat object has 244 cells, and when I proceed to cluster_cells after converting to cds, I get the following error
> cds
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Hello, I am trying to do a GSEA with MAST on my own data but I am following the tutorial "Using MAST with RNASeq: MAIT Analysis"
I could conduct the GSEA with the function gsea = gseaAfterBoot() …
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In seurat 5, all run quite well with logNormalize, but got an error after I changed to SCT normalization with FastMNNIntegration and scVIIntegration. The codes and errors I got please find below:
c…
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Hello, and thank you for taking the time to meet with us on the call before the holidays! The presentation from that call containing the background of MRI and MRIO as well as some use cases can be fou…
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After using the `SCTransform` function, I found that some of my variable features are not in `scale.data`. This is best illustrated in the example below. From other posts (https://github.com/satijalab…
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Hi, nice paper and thanks for sharing your code and data publicly!
I have a question about controlling for batch effect.
In `seurat_integration.R`, after you run `IntegrateData()`, you perform d…
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Hello,
I have a list of seurat objects that I read into a list. Then I merge them, split them by experimental condition, perform standard steps but when running the function FindIntegrationAnchors()…