Cell type deconvolution from Bulk RNA-seq data
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4 weeks ago
Anand ▴ 10

Hi everyone.

I have brain RNA-seq data and a number of significantly DEGs. I also have a list of marker genes for astrocytes, neurons, microglia, oligodendrocytes, endothelial cells. I've read in some papers that they use a one-sided fisher's test to do the cell type deconvolution analysis to find out which cell types are more affected than others. Does anyone have any code they could share or advice on how to do this?

Thanks.

cell-type RNA-seq digital cytometry • 259 views
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Take a look at the EPIC tool . it may help

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Thanks. I'll give it a go.

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4 weeks ago

Sound like just doing a Fisher's exact test for geneset enrichment. Most cell type deconvolution methods use the whole expression matrix/vector for sample and references.

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