Questions tagged [seurat]
Seurat is a package for analyzing single cell rna seq data.
149
questions
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2answers
48 views
Reading in external single cell data
I'm trying to read in an external single cell dataset from https://www.nature.com/articles/s41467-020-16164-1, but I am having trouble reading in the count matrix.
counts found here: https://www.ncbi....
0
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0answers
36 views
Error in colSums(cts[[i]]) : 'x' must be an array of at least two dimensions
I'm getting an error when creating the counts from a single cell experiment.I'm identifying shared barcodes as well as lowUMI barcodes with the follow code:
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1
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1answer
39 views
FindMarkers from Seurat returns p values as 0 for highly significant genes
I have been working on FindMarkers function for identifying significant genes in the cluster. But some Significant genes have very low p values, so they are returned as 0 in the output.Any value less ...
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0answers
24 views
CITEseq different sequencing depth normalization -- Seurat
New technician ruined his first 10X CITEseq experiment on cells counting level and the ratio between replicates is 14k:2.2k:0.8k ncells.
How should I now normalize protein data (ADT) from experiment ...
2
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3answers
60 views
In Seurat, how can I export cluster IDs to csv files
I am doing scRNAseq analysis with Seurat.
I clustered the cells using the FindClusters() function.
What I want to do is to export information about which cells belong to which clusters to a CSV file.
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2
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0answers
19 views
Calculating percent mouse cells per sample
I want to see the correlation between % mouse reads per sample vs % mouse cells per sample. I've already calculated the % mouse reads per sample but I'm stuck on calculating the % of mouse cells per ...
1
vote
1answer
26 views
Removing columns from meta.data in Seurat
I'm trying to remove columns from the meta.data from a Seurat object. Is there a way to do that or would I have to re-create the Seurat object without that column?
0
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2answers
79 views
ViolinPlot x-axis
I'm trying to set the x-axis in my Violin Plot to go by each patient rather than it being scattered.
...
0
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0answers
13 views
How to calculate species fractions in Seurat
I'm working with a PTX dataset and I'm trying to calculate species fractions based on read count instead of cell count.
Would just be a matter of taking the raw counts matrix of cells x gene per ...
0
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1answer
95 views
Subsetting a Seurat object based on colnames
I'm trying to subset my seurat object based on colnames. I have gone ahead and labeled each cluster and now I want to subset all the colnames that are in Cancer_human for human_colnames and all the ...
-1
votes
1answer
41 views
Problem with Seurat reference mapping
I have 10X scRNA-seq multiome's 3' poly-A capture (scRNA-seq+ATAC-seq) from PBMC
Using Seuratreference mapping, I mapped my scRNA-seq part on reference PBMC (for ...
1
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0answers
119 views
Understanding the dot plot from seurat
I am working with single cell data and using seurat to analyze the results. Often in manuscript, we see the dotplots showing the expression of the marker genes or genes of interest across the ...
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0answers
48 views
1
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1answer
34 views
Seurat - single cell analysis
I have been doing single cell analysis based on seurat and I realized after each clustering and reclustering when I run SCTransform, in my code there is vars.to.regress = percent.mt and I was running ...
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1answer
78 views
sctransform - mitochondrial expression filtering / transformation
I have a Seurat object which has a high expression of mitochondrial genes
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1
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0answers
84 views
Creating new seurat object with new matrix
I'm trying to do a cross-species comparison between the patient TME vs. the PTX TME to understand gene expression conservation. I have already converted between mouse and human genes giving me a ...
0
votes
1answer
63 views
Avoiding the warning 'The following features were omitted as they were not found in the scale.data slot for the SCT assay' in Seurat
I have a Seurat object
I want to plot a list of genes but I got a warning saying most of genes removed
I have tried with both my genes of interest and all variable genes but the results is very ...
0
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1answer
38 views
1
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1answer
367 views
converting mouse genes to human genes
I'm trying to convert mouse genes from PTX data to human genes in order to do a comparison with patient data to see what genes are being conserved. I'm using this file for the orthologs.
http://www....
0
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1answer
62 views
TCR-seq or scRNA-seq
I need idea, intuition, suggestion please
I have 10X scRNA-seq of PBMC (multiome's 3' poly-A capture), can I capture ...
0
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0answers
47 views
Making a box plot of the proportion of cells in each cell types in two groups
I have number of cells in three cell types T, B, M in a Seurat object
For two groups of patients, cancers and controls like
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1answer
106 views
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2answers
76 views
2
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1answer
120 views
SCTransform Warning: in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
Running SCTransform on my seurat object produces the warning:
Warning in theta.ml(y = y, mu = fit$fitted) : iteration limit reached
What does this warning mean? ...
0
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2answers
61 views
Merging two dataframes in R
I have a file with cluster number of a scRNA-seq and corresponding annotated cell type like
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-1
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1answer
58 views
Filtering cells from values in metadata
I metadata slot of Seurat object I have mapping score of each cell to a reference PBMC data like
...
0
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1answer
40 views
What does this Seurat argument mean
I have extensively read about percent mito in Seurat but I got more and more confused
Let's say we want to keep cells with ...
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1answer
111 views
Seurat Dimplot with different clustering IDs
In Seurat metadata I have assigned cells to some cell types with different resolutions
I have added the cluster identities to the object via Idents:
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1
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1answer
257 views
color by clusters and sampled in Seurat
I have a Seurat object
I want to have both cluster numbers and coloured cells by sample names like this figure (from a Nature paper)
I have tried group.by argument ...
0
votes
2answers
256 views
Adding metadata to Seurat object
I have a Seurat object of 8 patients. I want to add metadata to that so that I have origin of each cell. At the moment UMAP just shows a bunch of cells while I want to color clusters by sample
This is ...
1
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1answer
46 views
Seurat clustering Methods-resolution parameter explanation
I am learning the Seurat algorithms to cluster the scRNA-seq datasets. I found this explanation, but am confused. Can someone explain it to me, "The FindClusters function implements the procedure,...
0
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1answer
120 views
"variable.features.n" in SCTransform
Whats the role of "variable.features.n" in SCTransform function of Seurat? I try setting "variable.features.n" at three different numbers (2000, 5000, 10000). In the downstream ...
1
vote
1answer
44 views
The biological meaning of the random variables and the responses in Seurat analysis
In the Seurat analysis, if we suppose that Xg and Xr denote the random variables that associate to the expression level of the gene g and of the gene r, respectively. Let Y and Yv represent the ...
2
votes
1answer
46 views
Connection between Detected Genes and The Read Counts
I have been trying to understand the Seurat for analysing scRNA-seq data. It comes to my mind that the main data is organised in the Seurat object with rows as genes and columns as the cells, and the ...
-3
votes
1answer
93 views
Getting conventional gene symbol for Seurat [duplicate]
I have a Seurat object made by human single cells
I am mapping some genes on that but no sign of expression
When I GOOGLE for those genes I see the genes have different names
How I know Seurat uses ...
1
vote
1answer
50 views
Seurat - subsetting by genes expressed
Originally- I was looking if in at least one of these genes were expressed:
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1
vote
2answers
58 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
vote
1answer
39 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 ...
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votes
1answer
80 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
vote
1answer
70 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
184 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
35 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
153 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
votes
1answer
155 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
votes
1answer
733 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
165 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
331 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
vote
2answers
165 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
vote
1answer
97 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
627 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 ...
