All Questions
Tagged with single-cell seurat
61 questions
2
votes
1
answer
303
views
Why does my SplitDotPlotGG plot show differential expression of a gene but Seurat::FindMarkers() function does not return it?
I have analysed and clustered my single cell rna seq data with methods in the Seurat package. After clustering, I obtained two main clusters: 0 and 1. I used the Seurat SplitDotPlotGG function to ...
- 547
0
votes
1
answer
3k
views
how to obtain only one cluster's data (.csv file) in Seurat
I was using Seurat to analysis single-cell RNA Seq. And I was interested in only one cluster by using the Seurat. Does anyone know how to achieve the cluster's data(.csv file) by using Seurat or any ...
- 441
3
votes
2
answers
2k
views
Using Seurat to compare mutant vs.wt
I am interested in using Seurat to compare wild type vs Mutant. I don't know how to use the package. How can I test whether mutant mice, that have deleted gene, cluster together?
- 441
3
votes
2
answers
1k
views
Changing a wide range of colours to a limited gradient
I returned a FeaturePlot from Seurat to ggplot. My plot has a weird range of colours as below
I produced this plot by this code
...
- 2,232
3
votes
1
answer
2k
views
1
vote
1
answer
2k
views
Violinplot of gene expression
I have plotted the log normalized expression of two genes by violonplot for 4 clusters. I have links to my pictures and Seurat object too. My problem is this; in violin plot I can not see the mean or ...
- 2,232
3
votes
3
answers
6k
views
Mapping a list of cells in seurat featureplot
I have 209 cells, I clustered them by Seurat to 4 clusters. By Featureplot I am able to track a gene in clusters:
Higher color shows higher expression.
Now, for some genes I want to highlight some ...
- 2,232
7
votes
3
answers
16k
views
Finding the optimal resolution parameter in Seurat's FindClusters function
In Seurats' documentation for FindClusters() function it is written that for around 3000 ...
- 2,578
5
votes
1
answer
220
views
Which are the use cases for the methods for DE in Seurat
In Seurat we can specify multiple methods for finding DE genes.
I am wondering when should we use which one, the use cases. As ...
- 2,578
5
votes
2
answers
14k
views
Manually define clusters in Seurat and determine marker genes
I want to define two clusters of cells in my dataset and find marker genes that are specific to one and the other. Is there a way to do this in Seurat? Say, if I ...
- 2,578
4
votes
1
answer
3k
views
Subset on multiple genes in Seurat
I know that I can do subsetting on just one gene in Seurat:
...
- 2,578