Questions tagged [seurat]
Seurat is a package for analyzing single cell rna seq data.
98
questions
0
votes
0answers
15 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
votes
0answers
43 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
votes
1answer
17 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
votes
1answer
29 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
35 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
41 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
votes
1answer
38 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 ...
0
votes
0answers
16 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 ...
1
vote
1answer
25 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
96 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 ...
-5
votes
1answer
51 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
0
votes
2answers
89 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.
<...
0
votes
1answer
58 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
vote
1answer
28 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
55 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 ...
1
vote
0answers
104 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 ...
1
vote
1answer
163 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
votes
1answer
53 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
117 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
votes
1answer
55 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
votes
1answer
204 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
vote
1answer
167 views
Seurat FindMarkers() output, percentage
I have generated a list of canonical markers for cluster 0 using the following command:
...
0
votes
1answer
94 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
votes
0answers
36 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 ...
0
votes
2answers
277 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
107 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
0answers
121 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, ...
0
votes
1answer
126 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
votes
1answer
123 views
how to export the monocle data into Seurat
I have tried to export the monocle data into Seurat and got the error
...
0
votes
1answer
158 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
votes
1answer
790 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:
...
1
vote
2answers
552 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 ...
0
votes
0answers
44 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 ...
0
votes
1answer
91 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 ...
0
votes
1answer
447 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 ...
0
votes
3answers
361 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 "...
0
votes
0answers
104 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 ...
1
vote
3answers
230 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 ...
0
votes
0answers
821 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 ...
0
votes
0answers
74 views
how to cluster data separately based on HTO tags
If I have 2 samples hashed, ran together and generated one ADT file for them, then how do I plot 2 different ADT clusters separated based on the hashtags. I did use HTOdemux, but it shows me ...
0
votes
2answers
254 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, ...
1
vote
1answer
252 views
Hierarchical clustering for outlier detection - single cell RNASeq & WGCNA
I wish to conduct WGCNA on a single cell RNASeq dataset and, when choosing the optimal beta parameter after running pickSoftThreshold am presented with a rather ...
3
votes
1answer
530 views
Subsetting of object existing of two samples
I have a Seurat object existing of an aggregate of two samples namely; RD1 and RD2. I am trying to make a subset of each sample. But it's not really working. I manage to make a subset of the cells but ...
0
votes
0answers
33 views
How can I figure out the cluster that low express in a specific gene in Seurat?
I'm following the standard protocol of Seurat so far and I know that Seurat can display the cluster that high express in a specific gene, however, I want to display the cluster that low express in a ...
1
vote
1answer
2k views
DoHeatmap Hierarchical Clustering Seurat
I have a list of genes that I'd like to visualize using the DoHeatmap function in Seurat. However, the output of the heatmap does not result in hierarchical clustering and therefore makes it very ...
0
votes
1answer
240 views
Cluster is split in 2-3 locations on tsne plot - Suerat
I am running a single cell dataset (count data - exon) through Seurat. After running tsne I see a cluster (13) split in 3 different locations on the plot. Here are the commands I am running:
...
0
votes
1answer
128 views
Why is 42 the seed used in RunPCA() in Seurat?
The RunPCA() in Seurat 3.0 function has seed.use=42 by default. How does one choose a seed number? Is this chosen simply because ...
0
votes
2answers
593 views
How to create Seurat object while RNA expression and ADT combined into one matrix
I got an input matrix which RNA expression and ADT capture are combined into one file. I loaded the file into Seurat successfully, however, when I tried to create Seurat object, it threw out an error ...
2
votes
1answer
627 views
How to highlight specific cells in Seurat 2.4
I used Seurat 2.4 on our scRNA dataset to obtain the following tSNE plot.I was able to successfully extract cell IDs from the different clusters, and generate gene expression profiles. The analysis, ...
0
votes
3answers
727 views
Import gene list to Seurat to define cell types
Is there a way to import gene list into Seurat to define cell type? The default cell types in Seurat is not enough for our research. For example, we want to mark a subtype of B cells in Seurat, but ...
