User: Payal

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Payal90
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@payalpb_me
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Posts by Payal

<prev • 45 results • page 1 of 5 • next >
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Answer: A: Seurat FindMarkers avg_logFC for integrated dataset
... I also posted this query in Seurat Github issues page. Please follow the conversation here - https://github.com/satijalab/seurat/issues/3397 Summary: #first switch to RNA assay DefaultAssay(objecti) <- "RNA" object_RNA <- NormalizeData(object, verbose = FALSE) #then, find markers ...
written 4 weeks ago by Payal90
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Comment: A: Seurat DefaultAssay integrated vs RNA
... Can I ask I followup question - I need to first find markers for clusters for integrated dataset and the do Differential gene expression per cluster per condition. For that should I choose `DefaultAssay(combined.data) <- "integrated"` or `DefaultAssay(combined.data) <- "RNA"`. How will the re ...
written 4 weeks ago by Payal90
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Seurat DefaultAssay integrated vs RNA
... Hi, Whats the difference between the following in Seurat objects? DefaultAssay(combined.data) <- "integrated" & DefaultAssay(combined.data) <- "RNA" Thanks ...
R rna-seq sequencing written 4 weeks ago by Payal90
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Seurat FindMarkers avg_logFC for integrated dataset
... Hi, I am having trouble understanding the avg_logFC results of an integrated dataset (control and condition) in Seurat (3.1) for the FindMarkers pipeline. gene_name p_val avg_logFC pct.1 pct.2 p_val_adj gene1 0 -0.270265934 1 0.115 0 gene2 0 ...
R rna-seq sequencing written 4 weeks ago by Payal90
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Comment: C: Estimated Number of Cells in 10X vs Cells in Seurat
... Thanks a ton! Yes "filtered_feature_bc_matrix" makes sense and the numbers match. ...
written 6 weeks ago by Payal90
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Comment: A: Estimated Number of Cells in 10X vs Cells in Seurat
... I did this: sample1 <- Read10X("~/../outs/raw_feature_bc_matrix") sample1_seurat <- CreateSeuratObject(counts = sample1, min.cells = 3, min.features = 200, p ...
written 6 weeks ago by Payal90
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Estimated Number of Cells in 10X vs Cells in Seurat
... Hi, Why the "Estimated Number of Cells" and when I do dim(seurat_object) have different number of cells? **10X defines "Estimated Number of Cells" as "The number of barcodes associated with cell-containing partitions, estimated from the barcode UMI count distribution."** Eg:My sample in 10X summa ...
single-cell R sequencing written 6 weeks ago by Payal90
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Comment: C: DEseq three-group comparison
... So type_A_result means how A changes with B and C as reference right? Eg: if the Logfoldchange for Gene1 in type_A_result is 2.002, that means Gene1 is upregulated in A over B and C right? ...
written 9 weeks ago by Payal90
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Answer: A: FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
... I found this link. Its very well explained there too - https://hbctraining.github.io/scRNA-seq/lessons/sc_exercises_integ_marker_identification.html ...
written 3 months ago by Payal90
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Comment: C: Is Pseudotime analysis most applicable to time-series experiments?
... Thanks @piyushjo. I am working on a brain sample from SVZ region only at a single timepoint. I am using Monocle3 and am getting disjointed trajectories because there are so many different types of populations in the sample. ...
written 3 months ago by Payal90

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