Cell type deconvolution from Bulk RNA-seq data
2
0
Entering edit mode
2.8 years ago
Anand ▴ 40

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 • 1.6k views
ADD COMMENT
0
Entering edit mode

Take a look at the EPIC tool . it may help

ADD REPLY
0
Entering edit mode

Thanks. I'll give it a go.

ADD REPLY
0
Entering edit mode
2.8 years 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.

ADD COMMENT
0
Entering edit mode
22 months ago

Hi @ Anand

Was this working for you for for astrocytes, neurons, microglia, oligodendrocytes, endothelial cells? I see the tools need some gene expression reference profiles. I would like to do some cell deconvolutions the same fellows.

Cheers, Marcin

ADD COMMENT

Login before adding your answer.

Traffic: 2788 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6