User: roberts

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roberts30
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Posts by roberts

<prev • 26 results • page 1 of 3 • next >
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Making a UMAP from FCS file in R
... Hell! I've been asked to UMAP out of .FCS files in R (I know I can make it in Flow Jo but I specifically asked to make it in R). I have gated the cells to get CD8+ cells and am working with that. I am having a really hard time making a meaningful umap that gives anysort of information. So far this i ...
R umap flow written 22 days ago by roberts30
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FIltering Seurat clusters
... Hello I am trying to pull out CD8 T cell clusters from my seurat object. I am using the code CD8 <- CH005@meta.data[“seurat_clusters” %in% c(1,2,3,7,8),] But it keeps resturning an empty table. Does anyone have any suggestions? Thanks! ...
10x R rna-seq seurat written 7 weeks ago by roberts30 • updated 7 weeks ago by rpolicastro3.9k
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GLIPH version 2 question
... Hello I have TCR libraries from 10X prep. I am trying to compare the VDJ data to see if there is any similar/known sequences. I am trying to run it through GLIPH but I keep getting an error. The site says that > The format of TCR input file is tab-delimited, expecting the following columns in th ...
10x R tcr gliph rna-seq written 8 weeks ago by roberts30
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Comment: C: Integrating two Seurat Objects
... Thanks, I changed my code to DefaultAssay(patient.integrated)<- "RNA" patient.integrated.markers <- FindAllMarkers(patient.integrated, only.pos = TRUE, min.pct = 0.25, logfc.threshold = 0.25) patient.integrated.markers %>% group_by(cluster) %>% top_n(n = 2, wt = avg_logFC ...
written 11 weeks ago by roberts30
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Integrating two Seurat Objects
... Hello- I am trying two integrate two seurat objects of pbmc but am having some issues Sample1 <- readRDS("Desktop/final_data/Sample1.RDS") Sample1$sample <- "Sample 1" Sample2 <- readRDS("Desktop/final_data/Sample2.RDS") Sample2$sample <- "Sample 2" patien ...
rna-seq seurat written 11 weeks ago by roberts30 • updated 11 weeks ago by igor12k
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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 4 months ago by roberts30
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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 4 months ago by roberts30
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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 4 months ago by roberts30 • updated 4 months ago by jared.andrews078.6k
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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 4 months ago by roberts30
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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 4 months ago by roberts30

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