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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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Cholmod error 'out of memory' : Merging Seurat Objects

I am trying to merge Seurat class objects that contain transcriptome count data (sparse matrix). I am relatively new to R, so any help/solutions is appreciated. I have added a screenshot of the data I'm working with. **General…
Erudite
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R - match combinations of nested list values from an index and return value

Hi I have the two data sets. The first one is a list of genes linked to a given cluster (0-7): # gene output Cluster <- rep(0:7, each = 10) Gene <- c("LMO3", "NEUROD6", "NFIB", "SNAP25", "RTN1", "CPE", "SOX11", "CSRP2", "VAMP2", "ID2", "EMX2",…
Raf
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How to generalize umap parameters

The main parameters I am using to create the umap are min_dist, a and b. I have set min_dist=0.5, a=1, b=1 which is giving a meaningful low-dimensional representation for most datasets initially, when all the features are used (approx 10K to 30K…
rj dj
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transpose and rename dataframes in a for() loop in r

I have a list of files with the following pattern: sampleid_samplename_counts.csv representing count matrix with cellname in rows and genes in columns. I'm trying to generate count matrix from these files to load in the Seurat package that need…
Sebrw
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DoHeatmap function Seurat - Error in dataframe: arguments imply differing number of rows

I'm trying to use the DoHeatmap function in Seurat to show expression of a number of genes across some defined clusters. B_cells is my Seurat object. tfs <- c("PRDM1", "PAX5", "BACH2") DoHeatmap(B_cells, features=tfs) I'm getting this error…
Hannah Bradford
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how to make a subset of cells expressing certain gene in seurat R

I want to create a subset of a cell expressing certain genes only. Here is my coding but it always shows 'No named arguments passed' I have no idea how to correct that. Dbh.pos <- Idents(my.data, WhichCells(my.data, expression = Dbh > 0, slot =…
Elaine
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Replace value of a @slot in each element of a list of structurally identical S4 objects

I have a list of S4 objects of class Seurat, where each object has several slots: > lapply(seurat.objects, slotNames) $gw14 [1] "raw.data" "data" "scale.data" "var.genes" "is.expr" [6] "ident" "meta.data" "project.name"…
Carmen Sandoval
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How to plot multiple UMAPs in a specified grid such as 6 x 3?

I am using the new Seurat 3 package to analyze single-cell sequencing data. I have merged 18 Seurat Objects and have saved the individual identifiers in the meta.data. When plotting out the 18 individual UMAPs using the split.by argument in the…
Kimberly Burgess
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How to save an 'AI friendly' plot in R when using ggplot2?

When I save a tSNE plot with a large amount of points, I want to convert all the points in the plot to a PNG file while the remainder of the image (axes, labels, all text) remain as vector graphics. How could I do such things? (I know that the…
李子逸
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How to reorder cells in DoHeatmap plot in Seurat (ggplot2)

I'm plotting a heatmap with Seurat in R require(Seurat) data <- data.frame(cell1=c(-0.5, 0.5), cell2=c(-0.8, 0.3), cell3=c(2.0, 0.1), cell4=c(1.0, 1.0)) rownames(data) <- c("gene1", "gene2") test <- CreateSeuratObject(data) test@scale.data <-…
Nikolay Markov
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handling sequential tasks with purrr

I would like to take list of objects and build a single object out of all of them. The actual use case is to combine multiple Seurat Objects into a single object. Currently I use a for loop, however, I was curious if I could use purrr::map. To…
HowYaDoing
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Seurat, interfering with ggplot2/plotly output

I am writing an R script in Rstudio looking at single cell data and generating various graphs. The package I am using is ggplot2. It generates nice graph outputs like this when the Seurat library is not loaded: Then when the Seurat library is…
Te-Yo
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R syntax for Seurat ClassifyCells command

I am working with an R package called Seurat for single cell RNA-Seq analysis. I want to use a function of the package called ClassifyCells to add information about my various cell types to the data. But I am struggling to get the syntax correct…
Paul
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Regular Expression for hemoglobin genes

I'm quite new to R, seurat and scRNA seq analysis. Using the seurat package in R to analyse single-cell RNA sequencing data, I came across the option to analyse the percentage of hemoglobin-genes per cell. The code suggested in different tutorials…
KriBaLin
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Too Few Results in fGSEA analysis

I have been having headaches about this for a while now and I am hoping you can help me out. I am analysing scRNAseq datasets from mouse kidneys and got Differential Expression data from pseudobulking analyses (DESeq2 package) comparing sick vs…
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