User: mvis1231
mvis1231 • 60
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Posts by mvis1231
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... Hi I have two samples (control and knockout) of scRNA-seq data and I followed Seurat vignette to do the integrative analysis (https://satijalab.org/seurat/v3.2/immune_alignment.html).
I tried to find some genes with increased/decreased expression in clusters by comparing their "Avg_logFC" values fo ...
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... Hi, I did follow Seurat standard integration workflow for my previous single cell RNA-seq analysis (https://satijalab.org/seurat/v3.1/immune_alignment.html) and I am currently performing a reference-based integration analysis, following the "Reference-based" tab in the Seurat vignette of integration ...
written 6 months ago by
mvis1231 • 60
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... Wow.. This explanation is just amazing... I clearly understand now.. Thank you so much for the details, Jared. ...
written 7 months ago by
mvis1231 • 60
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... Hi, I am new to bioinformatics and I have a few silly questions about how to define thresholds for QC metrics in Seurat.
I noticed that Seurat filters cells that have unique feature counts over 2,500 or less than 200. And I have heard that we need to apply a different QC values for each dataset, by ...
written 7 months ago by
mvis1231 • 60
• updated
7 months ago by
jared.andrews07 ♦ 8.4k
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... Hi, I have data from a specific cell from mouse fed with a certain diet. I integrated 4 datasets that were measured at four different time for the integrated single-cell RNA seq analysis. I have been referring to the Seurat vignette : https://satijalab.org/seurat/v3.1/immune_alignment.html.
I am us ...
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... That's what I was asked, but I am also being confused.. If we calculate the sum of each column (each cell), then the number is nCount_RNA, right? ...
written 7 months ago by
mvis1231 • 60
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... Dear all,
I have been following this Seurat tutorial: https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html
When I do `quantile(object$nFeature_RNA)`, I can check the distribution of number of genes detected in each cell.
Also, `quantile(object$nCount_RNA)` gives me the distribution of number of ...
written 7 months ago by
mvis1231 • 60
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