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User: mvis1231

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mvis1231 • 60
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Posts by mvis1231

<prev • 7 results • page 1 of 1 • next >
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Barplot of genes deferentially expressed in a few clusters
... 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 ...
scrna-seq gene de seurat barplot written 4 months ago by mvis1231 • 60 • updated 4 months ago by swbarnes2 ♦ 9.4k
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Difference between Seurat standard integration workflow and Seurat reference-based integration
... 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 ...
scrna-seq reference-based integration seurat written 6 months ago by mvis1231 • 60
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Comment: C: QC metrics for each dataset in Seurat for scRNA-seq
... 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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QC metrics for each dataset in Seurat for scRNA-seq
... 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 ...
scrna-seq qc seurat written 7 months ago by mvis1231 • 60 • updated 7 months ago by jared.andrews07 ♦ 8.4k
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SingleR for integrated scRNA-seq analysis
... 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 ...
scrna-seq integrated singler assay written 7 months ago by mvis1231 • 60 • updated 7 months ago by igor ♦ 12k
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Comment: C: Distribution of cell numbers in Seurat
... 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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Distribution of cell numbers in Seurat
... 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 ...
scrna-seq R nfeature_rna seurat ncount_rna written 7 months ago by mvis1231 • 60

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