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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.

202 questions
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Add Metadata to Seurat Object

I am working with a R package called "Seurat" for single cell RNA-Seq analysis. I am trying to add metadata information about individual cell samples to the Seurat Object. But the downstream plotting commands are not working. I am wondering if…
Paul
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Odd behaviour of sample when subsetting Seurat objects

I am seeing a peculiar behaviour from the R Seurat package, when trying to subset objects to specific sets of cells. So, say that I generate three sets of random cell names from a Seurat object using…
nico
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R kernel crashes while loading R package using rpy2

First of all, I’m new to rpy2 / jupyter so please don’t judge me if this isn’t the correct place to ask my question. I am trying to set up an integrated workflow for data analysis using R and Python and I encounter the following error: I am on…
fkoegel
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Reticulate can't install python packages

I'm trying to run the Seurat pipeline in RStudio (Windows 10 , which requires having the python library 'umap-learn' installed (Seurat walkthrough: https://satijalab.org/seurat/v3.0/pbmc3k_tutorial.html). To install said library, I'm using the…
Lukas Vlahos
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Error in validityMethod(as(object, superClass)) : object 'Matrix_validate' not found

I just try to use : scRNA <- FindNeighbors(scRNA, dims = pc.num) and scRNA.counts <- Read10X(data.dir = "filtered_feature_bc_matrix") and both of them gives error like : Error in validityMethod(as(object, superClass)) : object…
bohrxd
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`doParallel` vs `future` while using `Seurat` package

Here is the story. From Seurat vignette, FindMarkers() can be accelerated by utilizing future package, future::plan("multiprocess", workers = 4) However, I am running a simulation that I need to use FindAllMarkers() inside a doParallel::foreach()…
yuw444
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UnsatisfiableError when trying to load r-seurat

I'm trying to make a very simple conda environment with just r-seurat as a dependency. My environment yaml looks as follow: channels: - bioconda dependencies: - r-seurat And I'm creating it with conda env create -n myenv -f envs/myenv.yaml I…
compuTE
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No slot of name "images" error when trying to open RDS file

I'm trying to open a file but it seems I'm running into an error. Here's what I'm doing, in RStudio: file <- readRDS("~/Downloads/file.rds") View(file) And then I get this error: Error in eval(call("@", object, slot)) : no slot of name…
JB_Probs
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R package 'Seurat' crashes with openMP error

I've been stuck in this problem for a while. I've installed a package Seurat on my Mac (Catelina), but when calling this library, R will crash with the following message: OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already…
Fei-man Hsu
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Aign 2D scatter plots (and link them?)

I occasionally see diagrams where two 2-dimensional scatterplots are superimposed on one another in a 3D space so that corresponding points can be linked. Frequently these take the form of networks where the two networks overlayed. For example: …
G_T
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Why does FindNeighbor from Seurat give "'CsparseMatrix_validate' not found" error?

This is the code that I want to run: Aldh1l1.neg_Atp1b2.pos_new <- FindNeighbors(Aldh1l1.neg_Atp1b2.pos_new, dims = 1:10) But it doesn't work due to this error: Error in validityMethod(as(object, superClass)) : object 'CsparseMatrix_validate'…
Yutiini
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Adding p-values to a violin plot in seurat

I currently have a seurat object scData in which I have applied module scored by using AddModuleScore. AddModuleScore(scData, features = inflam, name = "inflam_score", seed = 1, search = FALSE, assay = NULL, nbin = 21, ctrl = 100, pool = NULL) I've…
mmpp
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Merging CSV data frame to Seurat object metadata - values all changed to 'N/A'

I have processed a Seurat scRNAseq object with the CellTypist package (Jupyter Notebook) to annotate immune cell types. I managed to export the predicted cell labels as a CSV. I have read this into R and would like to merge the results as an Idents…
clb96
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How to Include Legend in Seurat DimHeatmap function

Is there a general way to include legends in Seurat graphs? For example, if my code is, DimHeatmap(norm_data3, dims = 1, cells = 500, balanced = TRUE) how can I include a legend with color corresponding to value of PCA component?
algebroo
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New ID column depending on another column in R

I want to generate a new ID column in my df based on another column my df looks something like this > TCR <- c("CAAETSGSRLTF;CASSQEGTGVYEQYF","CGSRLTF;CASSQEGTGVYEQYF","CAAETSGSRLTF;CASSQEGT", "CAAETSGSRLTF;CASSQEGTGVYEQYF") > df <-…
Ahmed Hassan
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