Questions tagged [seurat]
Seurat is a package for analyzing single cell rna seq data.
115
questions
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2answers
23 views
Positive marker and negative marker in scRNA-seq datasets
I am learning about the marker genes and clustering by Seurat in scRNA-seq datasets. However, I am confused about the term positive marker and negative marker. What I understand is the marker genes of ...
1
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1answer
27 views
Find selective markers for one cluster automatically
I detected all markers for each cluster and checked 20 top markers for my clusters one by one. Is there any way that I figure out the selective markers automatically from all the clusters?
For ...
-5
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1answer
58 views
Making Seurat object from a processed file [closed]
I have downloaded log2(TPM/10+1) values of 11,548 genes and 9609 cells from ...
1
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1answer
40 views
Clustering with Seurat
My data consists of two groups control and stim. I'm concerned that my clustering in the stim group is dominated by the unregulated genes. I can remove these genes and recluster but is there a way to ...
0
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0answers
80 views
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 ...
0
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0answers
33 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). ...
0
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1answer
52 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 ...
2
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1answer
92 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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-1
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1answer
325 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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0
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1answer
80 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 ...
0
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1answer
160 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 ...
1
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2answers
112 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 ...
1
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1answer
63 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 ...
1
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1answer
388 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 ...
0
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1answer
120 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 ...
1
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1answer
89 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 ...
2
votes
2answers
67 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 ...
0
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1answer
1k 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'...
0
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1answer
73 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 ...
0
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2answers
1k 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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0
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1answer
840 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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0
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1answer
366 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 ...
0
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0answers
53 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?
2
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0answers
65 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....
0
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1answer
823 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(...
0
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1answer
256 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 ...
1
vote
1answer
355 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 ...
3
votes
1answer
437 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/...
0
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1answer
133 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 ...
1
vote
1answer
90 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 ...
1
vote
1answer
587 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
387 views
Creating a Seurat object from a SingleCellExperiment object [closed]
Error in CreateAssayObject(counts = counts, min.cells = min.cells, min.features = min.features) : No feature names (rownames) names present in the input matrix
0
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2answers
660 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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3answers
445 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 ...
1
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1answer
213 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 ...
1
vote
1answer
94 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 ...
2
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0answers
352 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 ...
1
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1answer
741 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 ...
0
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1answer
95 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 ...
3
votes
2answers
194 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 ...
0
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2answers
886 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 ...
0
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1answer
691 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 ...
1
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1answer
274 views
Seurat FindMarkers() output, percentage
I have generated a list of canonical markers for cluster 0 using the following command:
...
1
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1answer
149 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 ...
0
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2answers
1k 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-...
1
vote
1answer
227 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 ...
0
votes
1answer
226 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 ...
0
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1answer
209 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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0
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1answer
425 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 ...
0
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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:
...
