Questions tagged [seurat]
Seurat is a package for analyzing single cell rna seq data.
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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
81 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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1answer
31 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
39 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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2answers
56 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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1answer
32 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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1answer
28 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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2answers
75 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
57 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
32 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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21 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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56 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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1answer
41 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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1answer
37 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
81 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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1answer
88 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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1answer
41 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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17 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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1answer
37 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
301 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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1answer
85 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
202 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
102 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
41 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
59 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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158 views
Understanding BuildClusterTree of Seurat
I am trying to understand how to use BuildClusterTree of Seurat to merge clusters. Being no informatics or statistical background, I am not understating how to use it. I am having the following ...
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1answer
262 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
61 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
138 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
92 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
272 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
208 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
109 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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39 views
How to find the differential gene expression between two samples
here are three samples' Dimplot. And I have a question about how to find the differential expression genes between Double-KO and Shox2-KO, for we can easily find the differential gene between the ...
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2answers
396 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
125 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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149 views
What means the negative sign on the colour scale when I use Seurat's DotPlot function to visualise gene expression in single cell rna seq data?
I wish to find out the meaning of the values on the average expression scale when one uses the Seurat DotPlot. If the scale represents the average expression per feature plotted per identity class, ...
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1answer
151 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
146 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
209 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
1k 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
759 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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0answers
52 views
How to set equal distances between axes ticks irrespective of number of points I plot in a ggplot?
how can I set an equal distance between the ticks of axes in a ggplot irrespective of the number of items I plot?
For example I want to have the kind of plot below from Seurat's ...
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1answer
98 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
603 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 ...
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3answers
481 views
Which correlation method to compute the correlation score between different clusters of Sc-RNAseq data?
I'm analyzing single cell rna-seq data and trying to compute the correlation score between different clusters. Wondering how to choose the correlation method("pearson" (default), "kendall", or "...
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0answers
123 views
Create a Heatmap that uses modules of genes rather than individual genes in Seurat
Is it possible to create a Heatmap in Seurat that takes in and displays modules of genes as its features rather than individual genes? So if I have a module of genes associated with a trait or ...
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3answers
296 views
Understanding Single Cell RNAseq Plots
I have just started some single cell RNAseq analysis with 500 cells. I have used Seurat for analysis. Following the guideline I have generated few plots. Now I am trying to understand how to read ...
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1k views
Create heat map that groups genes by expression within cluster in Seurat
I have a set of cells that I am performing Drop-seq on to look at cell expression. Among my heat maps for gene expression I want to be able to graph them similar to the graph below:
Where the cells ...
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2answers
285 views
how to generate an scRNA counts file
I have barcodes.tsv, genes.tsv and matrix.mtx file from my RNA seq data and I want to generate a scRNA counts files using R. When I tried using the readMM function, ...
