All Questions
Tagged with single-cell seurat
61 questions
0
votes
0
answers
21
views
Demultiplex double hashed cells using Seurat (R)
I am using Seurat to demultiplex my single-cell RNA data, which also has HTO data for hashing. Each cell is hashed once based off it's origin ie organ1, and then hashed based off the cell type ie cell ...
2
votes
0
answers
27
views
Find up/downregulated gene lists across scRNA-seq samples
I have two separate scRNA-seq datasets that are different batches. I want to get genelists of up/downregulation of one cluster in one dataset compared to another cluster in the other dataset.
I ...
2
votes
2
answers
1k
views
Convert ensemble genes to gene names in my sigle cell signature matrix annotated with seurat in R?
I have single cell data which I want to annotate with the seurat package, so I ran this code in R:
...
- 111
1
vote
0
answers
550
views
Loading scATAC-seq data containing matrix.mtx, fragments.tsv and barcodes.tsv files from GEO into R?
I want to analyse the single-cell ATAC-seq data from 10X downloaded from GSE158398. The files attached to this dataset are matrix.mtx.gz, ...
- 11
1
vote
2
answers
877
views
How to calculate cell type percentage in every sample
I have a Seurat object (metadata) with the single R samples consisting of cell types and sample types columns. I am trying to make a table that has a sample and percentage of cell types for each ...
3
votes
2
answers
2k
views
How to extend the x axis in Dimplot Seurat
I have performed a Seurat PCA via Dimplot.
How do I extend the x axis?
As you can see in my figure the double x axes overlap.
- 53
1
vote
2
answers
422
views
Error in dimnamesGets(x, value) when trying to read data using Seurat package
This question has also been asked on Biostars
I am trying to create a Seurat object using the package "Seurat". When I am reading my raw files using the function ...
- 21
0
votes
0
answers
505
views
extracting raw gene counts based on the cluster generated by seurat
I'm new to single cell sequencing analysis. I have made different clusters using seurat. Now I would like to extract the raw gene counts based on the cluster generated by seurat.
i have provided my R ...
1
vote
0
answers
167
views
Identifying highly variable genes in scRNA-seq: Seurat vs M3Drop
Following a single-cell RNA-seq workshop, I created a Seurat object (my_data), normalized the data, and then tried to identify highly variable genes using two ...
- 11
1
vote
0
answers
39
views
how to change the pseudo time trajectory direction?
Monocle is a comprehensive bioinformatics package which has the function to run the pseudo-time trajectory and changes in direction.
I wish to replicate this analysis. Like in the figure I would like ...
- 53
4
votes
2
answers
147
views
Does the number of RNA reads per cell obtained from the 10X scRNA experiment depend on amount of mRNA in given cell?
As we know, the amount of RNA reads per cell obtained from 10X scRNA experiment vary between cells. I wonder if this is effect of technical issues or does the number of RNA reads per cell obtained ...
- 43
2
votes
0
answers
353
views
Subsetting with harmony
Currently merged two Seurat objects together and then ran Harmony for batch correction. Now I want to subset out a cell type of interest do I re run harmony or just do the standard PCA?
...
- 391
2
votes
1
answer
985
views
Seurat Integration
I'm following the instructions for integration:
https://satijalab.org/seurat/articles/integration_introduction.html
And it's taking a while to run:
...
- 391
1
vote
1
answer
51
views
(scRNA-seq) I have a dataset with 4 conditions (experiments) should I be anchoring aka integrating data for each comparison when looking for DEGs?
I have an experiment with 4 conditions in it two of them are controls. When I am correcting for batch effects (either with PCA or CCA) should I restrict my comparisons between particular groups? So ...
- 400
1
vote
2
answers
1k
views
Assigning subcluster idents to original object
I have a scRNA-seq Seurat object I've analyzed, and I noticed that for some of the clusters, there's more than one cell type.
I've created a subset which and run FindClusters again to label the cell ...
- 51
2
votes
3
answers
5k
views
How to split a Seurat cluster in several subclusters?
I've analyzed my scRNA-seq data and have a couple of Seurat clusters that show more than one cell type in each cluster. (for example, cluster 9 shows both NK and CD4 cells)
How can I split a cluster ...
- 21
1
vote
2
answers
814
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....
- 391
2
votes
3
answers
3k
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.
...
- 27
0
votes
2
answers
2k
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.
...
- 391
0
votes
2
answers
2k
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 ...
- 391
0
votes
0
answers
296
views
1
vote
0
answers
217
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 ...
- 391
3
votes
2
answers
8k
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....
- 391
2
votes
1
answer
935
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,...
- 163
1
vote
1
answer
1k
views
Seurat - subsetting by genes expressed
Originally- I was looking if in at least one of these genes were expressed:
...
0
votes
1
answer
701
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 ...
- 17
0
votes
1
answer
1k
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 ...
- 105
1
vote
2
answers
722
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 ...
- 189
1
vote
1
answer
290
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 ...
- 547
0
votes
1
answer
2k
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 ...
- 17
2
votes
2
answers
172
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 ...
user9283
1
vote
1
answer
919
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 ...
- 17
0
votes
0
answers
154
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?
- 1
0
votes
2
answers
3k
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.
<...
- 391
2
votes
0
answers
1k
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 ...
- 189
3
votes
1
answer
515
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 ...
- 441
0
votes
2
answers
4k
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-...
- 441
1
vote
1
answer
1k
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 ...
- 441
0
votes
1
answer
499
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 ...
- 1
0
votes
1
answer
429
views
how to export the monocle data into Seurat
I have tried to export the monocle data into Seurat and got the error
...
- 441
0
votes
1
answer
282
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 ...
- 441
0
votes
3
answers
3k
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 "...
- 39
1
vote
0
answers
5k
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 ...
- 11
2
votes
4
answers
18k
views
how to merge more than two sample in Seurat?
I would like to merge more than two sample in the Seurat, and the mergeseurat can only merge two sample. So what should I do now. The screenshot is my script.
- 441
0
votes
1
answer
957
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:
...
- 133
1
vote
2
answers
2k
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 ...
- 31
2
votes
1
answer
2k
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, ...
- 21
2
votes
3
answers
3k
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 ...
- 31
2
votes
1
answer
1k
views
Which values from Seurat::FetchData function are to be used for correlation analysis between genes?
I want to perform a correlation test between genes in on my single cell RNA seq data set. I perfomed the differential expression analysis using the Seurat version 2 package, after performing stages of ...
- 547
2
votes
2
answers
387
views
Why are the clusters in the left side of a tSNE plot and not in the centre?
I have no idea why I used the subsetdata in Seurat after using CCA the TSNEPlot shows the cluster all in the left side and merge， did I miss something? Here are the code and figure I got.
...
- 441