Questions tagged [seurat]

Seurat is a package for analyzing single cell rna seq data.

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Retrieving Co expression data from a Seurat object

I know that this topic has been discussed in other threads, but I never found a definitive answers (and maybe there isn't one) about assessing coexpression in single cell data. I want to assess the ...
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25 views

Why could I be having only NAs for p_val and p_val_adj in Seurat DGE analysis?

I am doing a differential gene expression analysis to find out genes that are differentially expressed in one cell type from the lung in two conditions, control and idipathic pulmonary fibrosis (IPF). ...
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23 views

How do I change the identity of a sample from spatial 'Visium' data preprocessing in Seurat v3?

I'm wanting to create a merged object in Seurat using 2 10x Visium 'slices'. However, when I create an object, Seurat assigns an identity "SeuratProject" to the objects (by default I'm ...
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69 views

shiny code with seurat object

I am trying to create a shiny board for my scRNA seq data. I have saved my seurat objects adn I use following code as below: ...
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115 views

Visualizing FindMarkers result in Seurat using Heatmap

I used FindMarkers to find the DEGs between two clusters in my dataset using Seurat. I am trying to visualize the outcome using a heatmap but I failed to write the command in R. ...
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58 views

Calculating average mito.percentage for each cluster (seurat)

I have a tricky data set with cells that will have a higher percent of mitochondria genes than "typical" data sets. I would like to look at the mito percentage in each cluster without any ...
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85 views

Seurat Violin Plot: Why do dots align in one row?

I am analyzing a rather small scRNAseq dataset (39797 features across 3522 samples) and I have observed that dots in the violin plot are plotted in one line next to each other rather than in a cloud ...
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89 views

Single cell RNAseq cell cluster (true cluster or sub cluster)

I am trying to run seurat on ~5000 sinngle cells. I am expecting minimum 15 cell types to be present in the data. I tried to runn it with multiple conditions;I can see there is 27 clusters; I believe ...
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38 views

What is the best way to address the question of doublets and multiplets in a single cell RNA seq data set?

I have attached a histogram plot of the number of genes per cell in a single cell RNA seq data set of lung endothelial cells. I do not find a bimodal or multimodal distribution of the number of genes ...
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1answer
249 views

Seurat FindMarkers() output interpretation

I am using FindMarkers() between 2 groups of cells, my results are listed but i'm having hard time in choosing the right markers. Do I choose according to both the p-values or just one of them? If one ...
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51 views

Help with setting DimPlot UMAP output into a 2x3 grid in Seurat

On my merged seurat object of 6 samples, when I use the split.by function in tandem with the Dimplot/UMAP plot, all six samples are displayed in series along a commonly labeled 'UMAP_1' x-axis in an ...
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1answer
69 views

Differentially expressed genes analysis in Seurat

For the differentially expressed genes analysis, is it possible to check for DEGs based on the levels already identified in the object? For example, my dataset contains cells from 11 subjects, which ...
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62 views

How can I take cell number into account to find total RNA expression?

I'm hoping to quantitatively show differences in total RNA expression for a gene in a cluster of interest between different experimental groups. My exported average RNA values for each experimental ...
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372 views

Changing active.ident in Seurat

Im trying to change the active.ident to another column in metadata but this error keeps popping up! I recently upgraded to R version 4.0.2 from 3.6.1 The older version was working but the new one isn'...
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45 views

Seurat DE t.test

I am new to the Seurat package and was looking at the tutorials on the Seurat website and am just curious to know if there is any way to perform a t.test for the expression of a specific gene between ...
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659 views

Subsetting from seurat object based on orig.ident?

I am pretty new to Seurat. I want to subset from my original seurat object (BC3) meta.data based on orig.ident. however, when i use subset(), it returns with Error. ...
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1answer
418 views

How to add cluster name to metadata in Seurat?

I'm working on a Seurat object and want to name the clusters according to 2 values alone (yes/no). So I want to add a new column to metadata and annotate the clusters (UMAP) with it. ...
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1answer
221 views

Adding treatment groups via metadata to Seurat object?

I'd like to add metadata to 6 individual Seurat objects so that after I merge the objects into one, I can later label or split by using these identifiers. For example, I'd like to append an age group ...
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41 views

Seurat analysis only with matrix with no barcode and features

I have downloaded a dataset from GEO and only the matrix (mx) files are available. How can I perform the analysis without the barcode and the gene features?
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61 views

Clustering issue about overlapping CD4, CD8, and Foxp3 genes in mouse tumor models

bioinformatics scientists. I hope your work goes smoothly well and be safe. I'm stuck in trouble at the step of clustering. Briefly, I downloaded fastq files from a published study (https://www.ncbi....
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528 views

Error: Insufficient values in manual scale. 24 needed but only 1 provided?

folks. Can you give me idea about an issue that I encountered? I ran single-cell RNA sequencing data using Suerat in R, and when I tried to draw violin plot, there is an error as below. VlnPlot(...
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139 views

How to remove zero value of gene on FeatureScatter plot using Seurat?

Nowadays, I am trying to calculate Pearson correlation values between two genes of my interest from single-cell RNA-data (features.tsv, barcodes.tsv, and matrix.mtx files) which are obtained from the ...
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1answer
240 views

How to specifically select cluster on Featurescatter on Seurat?

Nowadays, I am trying to calculate Pearson correlation values between two genes of my interest from single-cell RNA-data (features.tsv, barcodes.tsv, and matrix.mtx files) which are obtained from the ...
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275 views

Receptor-Ligand R-package for visualization

I was wondering if there was any R-package for receptor-ligand interaction similar to SingleCellSignal (https://github.com/SCA-IRCM/SingleCellSignalR_v1/blob/master/SingleCellSignalR/vignettes/...
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79 views

Is it important to filter out poor quality cells before performing an integration analysis on single cell RNA sequencing data?

In order to perform an integration analysis of single cell RNA seq data, is it important to check the percentage expression of mitochondrial genes of cells as well as the feature counts to exclude ...
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34 views

Cell Ranger Aggr: How to properly use?

I have 4 samples (2 control, 2 treatment) and I have ran each individual sample through the CellRanger count pipeline. Now, should I use CellRanger aggr to combine the 2 controls and the 2 treatment ...
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66 views

What column and row naming requirements exist with Seurat (context: when loading SPLiT-Seq data)

I'm trying to use Seurat for the first time and am learning about single-cell analysis for the first time, and I'm doing so with split-seq data. (Full disclosure: I'm also a lightweight when it comes ...
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1answer
500 views

Why is library(Seurat) causing my R session to have a fatal error?

I recently tried to load library(Seurat) after installing Seurat package. It caused my R studio to have a fatal error and abort my session. I have successfully downloaded it before. I have uninstalled ...
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231 views

Creating a Seurat object from a SingleCellExperiment object

Error in CreateAssayObject(counts = counts, min.cells = min.cells, min.features = min.features) : No feature names (rownames) names present in the input matrix
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2answers
469 views

Adding certain barcodes to metadata in Seurat

I want to upload an excel file sheet that has certain barcodes that I would like to show on my umap. How do I go about adding the file and linking it to the metadata? Below is my following code. <...
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1answer
245 views

How to import data from cell ranger to R (Seurat)?

I will have some scRNA-seq data. The goal of the experiment will be to see if there is any difference in gene expression between treatment groups using the package Seurat from R. I have read a ...
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1answer
116 views

Set new Idents based on gene expression in Seurat and mix n match identities to compare using FindAllMarkers

I am relatively new to Bioinformatics and scRNA-seq data analysis. I am using Seurat V3 to analyze a scRNA-seq dataset in R. Currently, I have merged three scRNA-seq samples from the same donor into ...
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1answer
86 views

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 to where it shows the umap with the different clusters but I want to show where the ptx samples ...
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293 views

Understanding BuildClusterTree of Seurat

I am trying to understand how to use BuildClusterTree of Seurat to understand the relationship between clusters. Being from neither a bioinformatics or statistical ...
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1answer
531 views

Reading multiple raw files in Seurat

I have multiple single cell samples to analyze and I'm following the instructions in Satija Lab's website. I want to merge all the count files from all the samples at once, and associate the metadata ...
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1answer
77 views

Seurat clusters

I'm trying to show cell cycle regression and input sample metadata to my umap. I've been following Satija Lab's tutorials and have generated my umap but now want to specify which sample corresponds ...
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2answers
170 views

Differential gene expression bias due to effect of an individual sample

I am analysing a human single cell RNA seq experiment, where we have 4 groups, four samples each. Data has been analysed using Seurat, with the canonical workflow. I have tried DE using various ...
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1answer
467 views

Percentage of each cluster in Seurat

I am using Seurat to analyze my single cell data. I have 2 conditions, treated and untreated. I am trying to create a stacked bar graph in order to show the differences in cell types for each ...
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1answer
465 views

Seurat define manually a cluster and find markers

I am aware of this question Manually define clusters in Seurat and determine marker genes that is similar but I couldn't make tit work for my use case. So I have a single cell experiments and the ...
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1answer
245 views

Seurat FindMarkers() output, percentage

I have generated a list of canonical markers for cluster 0 using the following command: ...
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1answer
131 views

Finding differentially expressed genes between two samples

Hi, I was wondering whether we can find the differentially expressed genes between the Double-KO and the Shox2-KO. For the ...
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2answers
793 views

how to change the UMAP use in the dimplot and feature plot

I would like to know how to change the UMAP used in Dimplot and FeaturePlot from Seurat: how we can get the x-axis and the y-...
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1answer
186 views

how to change the PC use in the dimplot and feature plot

I would like to know how to change the PC use in the dimplot and featureplot by using Seurat. for we can get the x-axis and the y-axis like PC-1 and PC-2, if I want to use PC-4 and PC-5. How to modify ...
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1answer
188 views

Clustering information saved in Seurat object

Seurat V2 had a option to find clustering information saved in object: PrintFindClustersParams(object = pbmc). How can I get the same clustering parameters from objects in Seurat3? Do I need to ...
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1answer
184 views

how to export the monocle data into Seurat

I have tried to export the monocle data into Seurat and got the error ...
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1answer
322 views

Putting cells in Seurat dimplot selectively

I am going to adjust Seurat dimplot in a way avoiding some cells so both my dimplot and heatmap look nice If you please consider this picture, you would see some cells are far from the clusters so I ...
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1answer
2k views

Seurat VlnPlot presenting expression of multiple genes in a single cluster

Seurat VlnPlots are most commonly used to visualize differences in any given gene expression across multiple clusters or cell types. For example: ...
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2answers
1k views

Trim Seurat object to contain expression info only for selected genes

I'm working with some large Seurat objects (MOCA, MCA, Tabula Muris) studying gene coexpression, and I'm running into memory issues. Is it possible to remove all genes in a Seurat object that are ...
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1answer
117 views

different gene expression in the monocle

As it is shown in the picture that we can get the pseudotime plot by using Monocle. I was wondering whether we can use some function like the Seurat FindMarker to find out the differential expression ...
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1answer
993 views

How do I increase the minimum dot size in Seurat's DotPlot function?

I want to use the DotPlot function from Seurat v3 to visualise the expression of some genes across clusters. However when the expression of a gene is zero or very low, the dot size is so small that it ...