User: roberts

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roberts20
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Posts by roberts

<prev • 21 results • page 1 of 3 • next >
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Comment: C: Doublet in scRNA-seq
... I know it may not seem like it but I actually do spend a long time trying to find an answer before I post a question. I am new to bioinformatics and computer science as a whole. I get very lost very quickly, and I don't have access to anybody to answer my questions-- hence my use of this public for ...
written 16 hours ago by roberts20
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Doublet in scRNA-seq
... Hello, I did 10X scRNA-seq I want to filter out any doublets since we had a high number of cells read. Does anyone have any suggestions?I tried DoubletDecon but I am not familiar with shiny so could not figure out how to use it. Thanks! ...
R rna-seq seurat written 19 hours ago by roberts20
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Removing RBC contamination in Seurat
... Hello! I got data back from cellranger output. It is obvious in it that there is significant RBC contamination. There is some hemoglobin genes (HBA, HBB, HBD, etc) among the significant genes of clusters. Is it possible to filter out cells expressing these genes in Seurat? Thanks! ...
R seurat rna-seq written 20 hours ago by roberts20 • updated 19 hours ago by jared.andrews077.6k
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error in installing Seurat V. 4
... Hello, I have been trying to download Seurat 4.0 with the command they gave -- `remotes::install_github("satijalab/seurat", ref = "release/4.0.0")` But I keep getting a list of packages to update. I have tried all the 36 options but the end result is always that installation failed because unable t ...
R seurat written 2 days ago by roberts20
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Comment: C: Adding UMAP coordinates to metadata
... Thank you for your help. Just a follow up question how do I add PC to the meta.data (sorry I am new to coding). Thank you! ...
written 13 days ago by roberts20
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Adding UMAP coordinates to metadata
... Hello, I want to store my umap coordinates in my seurat objects meta.data. The umap coordinates are saved in my Object under reductions in cell.embeddings. How would I add this to the meta.data? I tried running AD007[["coordinates"]]<--AD007@reductions$umap@cell.embeddings I keep getting t ...
R seurat written 14 days ago by roberts20 • updated 14 days ago by fracarb850
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(Closed) Top 10 clonotype frequency
... Hello I am using top10_clonotype <- table(AD007S$clonotype_id) top10_clonotype <- as.data.frame(top10_clonotype) top10_clonotype <- slice_max(top10_clonotype, order_by = top10$freq, n=11) I am trying to pick out the top 10 most frequent clonotypes in my object. This code was wo ...
10x R seurat written 23 days ago by roberts20 • updated 23 days ago by genomax91k
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Mapping clonotypes on UMAP
... Hello! I have a suerat object and I would like to map the top 10 clonotypes in it. I am using the code top10 <- head(VariableFeatures(Object$clonotype_id),10) I keep getting the error, "Error in UseMethod(generic = "VariableFeatures", object = object) : no applicable method for 'VariableF ...
R clonotype rna-seq umap seurat written 26 days ago by roberts20
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Comment: C: TCR analysis in Suerat
... Hello, Thank you very much for all your help, you got it to work! Also sorry for all the confusion/hassle if you couldn't tell I am new to this and you've been a great help! ...
written 28 days ago by roberts20
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Comment: C: TCR analysis in Suerat
... Yes of course. Here is the full script- AD007.data <- Read10X(data.dir = "/Users//Desktop/AD007") AD007S <- CreateSeuratObject(counts=AD007.data, Project="CSF",min.cells = 2, min.features = 200) ### adding VDJ data AD007S_clonotype<- read. ...
written 28 days ago by roberts20 • updated 28 days ago by jared.andrews077.6k

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