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Questions tagged [seurat]

R package for analyzing Single Cell RNA-seq data

Seurat is a R package meant for quality control, analysis, and exploration of single cell RNA-seq (sequencing) data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data.

See also:

References:

Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, III WMM, Hao Y, Stoeckius M, Smibert P, Satija R (2019). “Comprehensive Integration of Single-Cell Data.” Cell, 177, 1888-1902. doi: 10.1016/j.cell.2019.05.031, https://doi.org/10.1016/j.cell.2019.05.031.

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Create a hierarchical clustering dendrogram for integrated Seurat object in R?

Does anybody know how to create a dendrogram for an integrated Seurat object. I can do it for a non-integrated object, but when I try: immune.combined <- BuildClusterTree(object = immune.combined, slot = "data") I see the error: Error in hclust(d =…
4DtyU
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R) Convert Seurat object to URD

I am a beginner in R trying to analyze my scRNA-seq data with URD to draw a tree. For this, I want to convert my seurat object to URD. So I followed a scripted written by Jeff Farrell below. base.path <- "~/urd-cluster-bushra/" # Load Seurat object…
Juhee Jeong
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Error in NormalizeData.default running DoubletFinder on an integrated seurat object in R

I'm trying to run DoubletFinder on a seurat object resulting from the integration of various datasets. The Seurat object has 2 assays: RNA & integrated. The integrated seurat object have been fully processed: Normalization and FindVariableFeature…
Sebrw
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Way to Make a Better Looking Dendrogram than in Seurat?

I'm trying to make a hierarchical clustering tree from the clustering produced by Seurat's clustering function. Their functions, BuildClusterTree and PlotClusterTree, produce a frankly ugly tree based on SNN (shared nearest neighbor) algorithm that…
montyman14
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Why does pdf() plot, dev.off() succeed but the same commands within a function call fail?

The following set of commands will print an appropriately formatted pdf file with the data represented, and this is the documentation for Dimplot. It runs appropriately and all the required packages load fine. project_name<-"my_project" file_stem<-"…
Sarutahiko
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PercentageFeatureSet() on several seurat objects

I have many seurat objects created from count matrixes downloaded from GEO. I want to use the PercentageFeatureSet() function on each of them to calculate the %MT. I tried : for (i in seu.list) { get(i)[["percent.mt"]] <-…
Sebrw
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retreive Seurat object name in R during a for loop

I'm working on single cell rna-seq on Seurat and I'm trying to make a for() loop over Seurat objects to draw several heatmaps of average gene expression. for(i in c(seuratobject1, seuratobject2, seuratobject3)){ cluster.averages <-…
Sebrw
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Subset a complex sparse matrix based on a logical column

I'm working with a Seurat object, and after doing some quality control I have a column of metadata called discard containing TRUE or FALSE based on whether the row in question failed QC and should be deleted. How do I do this? I have tried all the…
lilak95
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load data error (Read10X, Seurat - Guided Clustering Tutorial)

I am trying to follow the tutorial from Seurat website. https://satijalab.org/seurat/v3.1/pbmc3k_tutorial.html I got an error when loading the data. Load the PBMC dataset pbmc.data <-…
cicicamus
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umap highlighting two different models

I'm trying to create a umap for single cell data from human samples and ptx samples. I can get the umap plot showing the different clusters but I want to show where the ptx samples and human samples are. My code is as follows: #create the Seurat…
mmpp
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Error in eval(expr = expr) : object 'nFeature_RNA_lower' not found

I am extremely confused as to why this code keeps throwing an error. qc_and_normalize <- function(seurat_object, coeff=3) { nCount_RNA_upper <- median(seurat_object@meta.data$nCount_RNA) + coeff*mad(seurat_object@meta.data$nCount_RNA) …
Ani Khachatryan
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Change the y limits ( especially the minimum) with Vlnplot

I would like to draw a violin plot from my single cell data. I am using this function : Vlnplot(object, features, cols = NULL, pt.size = 0.1) But I would like to change the y axis to 3000-10000 instead of 0-70000. They only propose to change the y…
Juliette Leon
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Getting only the rownames containing a specific character - R

I have a Seurat R object. I would like to only select the data corresponding to a specific sample. Therefore, I want to get only the row names that contain a specific character. Example of my differences in row names: CTAAGCTT-1 and CGTAAAT-2. I…
ageans
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In storage.mode(from) <- "double" : NAs introduced by coercion

I am using Seurat and trying to analyze the data set that installed from GEO. But I am getting the following error. I am trying the tSNE plot using R and Seurat, but I received the error message about…
Ryo
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Error while trying to make a singleR seurat object

I have been trying to fix this problem but have come up empty all day. While trying to make this object singleR = CreateSinglerSeuratObject(counts = counts, annot = metadata, …
csmccaulec
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