User: cook.675

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cook.67540
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Posts by cook.675

<prev • 55 results • page 1 of 6 • next >
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Calling gene names from a list within Seurat subset function
... I have a list of 5 cytokines here: cyto <- c("Ccl1", "Ccl2", "Ccl3", "Ccl4", "Ccl5") I'm trying to get the subset function in Seurat to subset based on the expression level of one of these without referring to the actual gene name in the function. For example, here is the typical way: ...
seurat rna-seq written 3 months ago by cook.67540
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Comment: C: How to extract a specific gene sequence for a specific cell from scRNA-seq fastq
... Thanks for that link, one quick question: All the reads we have are transcript reads, I could then map to the transcriptome instead of the genome? Im going through this now, I created the SAM file from paired end fastq's following this tutorial: [https://icb.med.cornell.edu/wiki/index.php/Elemento ...
written 7 months ago by cook.67540
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Comment: C: subsetting out cells from seurat object based on expression of 1 gene
... sorry for the late reply, yes a vector, I created it by entering the following: gene.list <- c("GeneX", "GeneY", "GeneZ") It works if I type out each gene as follows: Object.subset <- subset(Object, GeneX > 0 & GeneY > 0 & GeneZ > 0) Anytime I try to pass a gene n ...
written 7 months ago by cook.67540
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How to extract a specific gene sequence for a specific cell from scRNA-seq fastq file
... I have a scRNA seq experiment where I would like to look at the raw sequencing data for one specific gene. We have 3' ends, and the sequence may or may not be different depending on the cell type we are looking at. I have the list (barcodes) from the cells we are interested in looking at, to see ...
scrna-seq sequencing written 7 months ago by cook.67540 • updated 7 months ago by mahmoud.s.fahmy0
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Comment: C: subsetting out cells from seurat object based on expression of 1 gene
... Thanks thats much simpler and more elegant. I have a follow up if you wouldn't mind: How would I subset a list of genes based on the same criteria? I tried: subset(object, features = gene.list > 0) And got an error here: Error: Under current subsetting parameters, the default assay w ...
written 7 months ago by cook.67540
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Comment: C: How to combine seperate seurat meta.data ID;s into one column?
... Thanks for the hint. I tried: object$exp <- AddMetaData(object, object$cond == "VEH1", col.name = "VEH") and got returned an error. [But I found the solution here!!][1] [1]: https://github.com/satijalab/seurat/issues/2081 ...
written 7 months ago by cook.67540
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How to combine seperate seurat meta.data ID;s into one column?
... I have an integrated object with 4 data sets (Veh1, Exp1, Veh2, Exp2) These tags are appended in the object meta data under object$cond What I would like to do is create a new metadata column called "exp", and label any cell that was labeled as Veh1 or Veh2 as VEH and any cell that was labeled as ...
scrna seurat written 7 months ago by cook.67540 • updated 7 months ago by RamRS27k
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appending information to seurat object meta.data
... I have a seurat object called AllCells.combined, and I wish to identify within the object all the cells that have expression of gene "Ighm" > 0; and also identify all cells that have expression of "Ighm" = 0 An easy way to do this would be to append it to the meta.data but I can't quite get it. ...
scrna seurat written 7 months ago by cook.67540 • updated 27 days ago by atakanekiz250
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A brief question regarding regressing out cell cycle effects or ribosomal/mitochondrial genes
... Im using the Seurat platform on some data but I think the question applies regardless of platform: I'm seeing some PC's grouped on cell cycle, and also notice hetergenous cycle stage grouping of cells in the PC plot If I call vars.to.regress within ScaleData to regress these out, does this only af ...
seuart scrna seq written 8 months ago by cook.67540 • updated 8 months ago by jared.andrews076.2k
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Comment: C: DEG data per-cell
... Thanks for that suggestion! Also, I was going to use the raw counts for this, but I don't understand why it would be incorrect to use normalized counts in this particular instance? One thing I dont understand still is when its appropriate to use raw vs. normalized counts ...
written 8 months ago by cook.67540

Latest awards to cook.675

Popular Question 6 months ago, created a question with more than 1,000 views. For subsetting out cells from seurat object based on expression of 1 gene
Popular Question 6 months ago, created a question with more than 1,000 views. For Pull number of cells in cluster from seurat object
Popular Question 6 months ago, created a question with more than 1,000 views. For Seurat DefaultAssay "integrated" or "RNA" with integrated dataset????
Rising Star 7 months ago, created 50 posts within first three months of joining.
Scholar 8 months ago, created an answer that has been accepted. For A: How to remove entire rows from seurat object based on cellhash read
Scholar 9 months ago, created an answer that has been accepted. For A: How to remove entire rows from seurat object based on cellhash read

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