Deconvolution using cibersortx, help with real example
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3 months ago
Dyno • 0

Hello Biostars,

I have been stuck on an issue for quite some time now, and I hope someone can help me or point me in the right direction. I've received my bulk RNA fastq files and analyzed it in R using DESeq2. I have found an article that provide snRNA-seq data that I have heard I can use to perform deconvolution of my bulk data, the article is here: https://www.sciencedirect.com/science/article/pii/S0092867422015239?via%3Dihub and this is the link to the snRNA-seq data: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE207848.

As I can see on CIBERSORTx I need to download or build a signature matrix off of this scRNA-dataset. I find this step quite challenging, and would very much appriciate if anyone could help me understand how to build a signature matrix file from this scrna-data.

Thank you very much in advance.

CIBERSORTx for reference: https://cibersortx.stanford.edu/tutorial.php

deconvolution cibersortx • 240 views
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