Question: Evaluate single cell data to look at combinations of gene expression within single cells
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gravatar for stellaparker
9 months ago by
stellaparker10
stellaparker10 wrote:

I have a large single cell data set and I am interested in a certain set of approx 50 genes and I want to evaluate in which combinations that they are expressed within single cells. For example: Cell 1 expresses: gene 1, gene 3, and gene 4 Cell 2 expresses: gene 1, gene 8, gene 18, and gene 17

and then I would like to produce a graph to visualize the combinations that occur or the combos that occur the most (with 50 genes, it is a lot of possible combos, I'm aware)

Does anyone know of any tools to accomplish this? Or a combination of steps I could take to cluster in such a way?

rna-seq analysis scrna-seq • 384 views
ADD COMMENTlink modified 9 months ago by singlecell0 • written 9 months ago by stellaparker10
0
gravatar for singlecell
9 months ago by
singlecell0
Norway
singlecell0 wrote:

You can coexpression networks for cells using WGCNA https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/

ADD COMMENTlink written 9 months ago by singlecell0

Using WGCNA requires at least 20 samples. Also WGCNA analysis is not "stable", which means that the another researcher will find impossible to reproduce the results of WGCNA analysis without having the original script where the WGCNA analysis was done. Also at a close inspection it looks like may modules are generated by chance.

ADD REPLYlink written 9 months ago by enxxx23230

Do you have another suggestion for how I could try to assess this?

ADD REPLYlink written 8 months ago by stellaparker10
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