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Questions about techniques in which the genetic material of a single cell is analysed individually

5 votes
1 answer
188 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 I understand, whole Seurat package is used for single cell sequencing an …
5 votes
3 answers
13k 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 cells the resolution parameter should be from 0.6 and up to 1.2. I am wondering then what should I use if I hav …
5 votes
2 answers
11k 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 produce two subsets by the SubsetData …
6 votes
Accepted

Subset on multiple genes in Seurat

I was able to achieve this in the following way: require(data.table) cell_names <- vector(mode="character") for (i in 1:length(neuron_ids)) { seurat_subset <- SubsetData(seurat_object, subset.name …
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: seurat_subset <- SubsetData(seurat_object, subset.name = neuron_ids[1], accept.low = 0.1) However, I want to subset on multiple genes. Is …