Questions tagged [seurat]

Seurat is a package for analyzing single cell rna seq data.

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5
votes
2answers
9k 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 ...
0
votes
1answer
1k views

R studio failed to install the latest development version of hdf5r from Github (win10)

I install hdf5r following https://github.com/hhoeflin/hdf5r, it shows two methods: When I use the second method to install from github,it showed many errors: ...
2
votes
1answer
5k views

Seurat with normalized count matrix?

I know that in Seurat we have the function CreateSeuratObject from which the analysis starts, but it accepts raw count matrix ...
5
votes
3answers
10k views

Resolution parameter in Seurat's FindClusters function for larger cell numbers

In Seurats' documentation for FindClusters() function it is written that for around 3000 ...
3
votes
1answer
1k views

How to set the position of groups in a Seurat object on a FeatureHeatmap plot

I am analysing singe cell sequence data and I have followed this tutorial, https://satijalab.org/seurat/pbmc3k_tutorial.html to perform QC and various differential analyses using the Seurat package on ...
3
votes
1answer
3k views

RunUMAP in Seurat not working: module 'umap' has no attribute 'UMAP'

I am trying to run UMAP in the following way: ...
1
vote
1answer
3k 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'...
1
vote
1answer
153 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 ...
1
vote
1answer
90 views

Enrich for genes expressed in the plasma membrane

I have a list of cell markers differentially expressed between 2 groups of cells, that I got with the FindMarkers command in Seurat. I want to enrich for those genes that are expressed in the cell ...
0
votes
2answers
126 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 ...
0
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2answers
69 views

Help with Seurat QC ambiguity

I have four PBMC samples from 10X scRNA-seq ...
0
votes
1answer
625 views

How to set new identities for new clusters based on a gene expression in Seurat?

I have a group of cells that have yellow (EYFP) expression and cells that don't. I want to define the yellow and non-yellow genes in two cell identities. I clustered the cells and then created Violin ...
0
votes
1answer
189 views

Differential expression between two types of cells of specific marker gene expression

I want to define the identity of some cells based on a gene marker (for example the colour yellow< EYFP gene). One group of cells has the EYFP gene the other doesn't and I want to find the ...
-1
votes
1answer
58 views

sctransform - mitochondrial expression filtering / transformation

I have a Seurat object which has a high expression of mitochondrial genes ...