User: roberts

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roberts30
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Posts by roberts

<prev • 21 results • page 2 of 3 • next >
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Comment: C: TCR analysis in Suerat
... Hello I have seemed to include the clonotype_id, aa sequence, and nt sequence. My isse now is that when I go to create a .csv I get this error "Error in as.data.frame.default(x[[i]], optional = TRUE) : cannot coerce class ‘structure("Seurat", package = "Seurat")’ to a data.frame". I cant seem to ...
written 9 weeks ago by roberts30
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Comment: C: TCR analysis in Suerat
... Thank you! I ran your code and the error messages went away. The only thing is that in the new CSV file under clonotype_id it says none for every barcode. Also is there a way to add in the aa sequence and nt sequence that I got from the cellranger output from the VDJ library prep. Thank you for taki ...
written 9 weeks ago by roberts30
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Comment: C: TCR analysis in Suerat
... Hello again, when I plug in say T8.meta <- T8[["clonotype_id"]] i get this error message "subscript out of bounds" and that seems to be the same for everything I plug into the brackets ...
written 9 weeks ago by roberts30
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Comment: C: TCR analysis in Suerat
... Thank you for your help it is greatly appreciated. I still have some questions though. It seems that the command T8 <- WhichCells(object, expression= CD8A >1) only saves barcodes. Is there a way to also get it to save TCR data (mostly clonotypes, aa sequence, and nt sequence). Also what is the ...
written 9 weeks ago by roberts30
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TCR analysis in Suerat
... Hello, I have successfully add my VDJ data to my GEX data by adding it as meta data. I would now like to distinguish between CD8 and CD4 TCR. I know by using WhichCell, I can pull out cells that express CD8 (T8 <- WhichCells(object, expression= CD8A >1)). I would then like to take that T8 dat ...
10x R tcr rna-seq seurat written 9 weeks ago by roberts30 • updated 9 weeks ago by jared.andrews078.0k
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cluster identification in seurat
... Hello is there a program to define cell clusters or cell types in seurat or is the best option to look at gene expression maps and name the clusters yourself? Thank you! ...
scrna-seq R seurat written 9 weeks ago by roberts30 • updated 9 weeks ago by jared.andrews078.0k
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Two different library preps
... Hello I have to combine two data sets from 10x in seurat. one data set was prepared following 5' library prep and the other was prepared following 3' library prep. I am trying to follow this [vignette from Seurat](https://satijalab.org/seurat/Seurat_AlignmentTutorial.html). The issue is that I can't ...
10x R seurat rna-seq written 9 weeks ago by roberts30 • updated 9 weeks ago by swbarnes29.2k
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Color code samples
... Hello, I have a merged seurat object with 3 different samples in it. How would I do about color coding for sample type. For example I want a umap where each of the 3 samples have its own color so you can see overlap/lack of overlap. Thank you! ...
R seurat rna-seq written 9 weeks ago by roberts30 • updated 6 weeks ago by Biostar ♦♦ 20
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pulling out TCR data
... Hello! I have successfully loaded my VDJ data into my seurate object. Once I have identified the cluster of CD4 and CD8 I want to be able to pull out all the VDJ barcodes, sequence, clonotype, etc. I saw that WhichCells() command lets you pick out cells that have a certain experssion, but when I do ...
R tcr vdj seurat rna-seq written 10 weeks ago by roberts30
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Analyzing TCR clonotype in Seurat
... Hello, I have merged my VDJ data into my Seurat object by adding it as metadata. Now is there a way to for example pull out of the CD8 TCR data and look at those clonotypes vs. CD4 TCR. How would you go about looking at different clonotypes in Seurat. Thank you! ...
10x R tcr rna-seq seurat written 10 weeks ago by roberts30 • updated 10 weeks ago by jared.andrews078.0k

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