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pllittle / CSeQTLworkflow

This readme repository contains sample codes for executing steps within our manuscript
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Some questions about using CSeQTL #1

Open zhangpicb opened 1 year ago

zhangpicb commented 1 year ago

Dear @sunway1999 @pllittle @liusi2019

Thanks for your beautiful codes and the CSeQTL paper!

I want to run some example data to make sure that I can use CSeQTL correctly.(PS. our lab own CMC and GTEx data) And I don't find Brain cell type deconvolution signature data.It would be appreciated if the signature data could be shared.(maybe .rData or .RDS file) I want to use CSeQTL to find cell type specific eQTL in my data.And I don't know how to get residual TReC PCs.

Best, zhang

sunway1999 commented 1 year ago

Hi, zhang, thanks for your interest in using CSeQTL. I have added the exact file name in the README file in the deconvolution section. here is the link: https://github.com/Sun-lab/scRNAseq_pipelines/blob/master/MTG/signature_MTG.rds

zhangpicb commented 1 year ago

Dear @sunway1999 @pllittle

Thanks for your reply!

https://github.com/pllittle/CSeQTLworkflow/blob/df7e852100dbf2986e2dd84f8c8e928aa18e5a7e/README.md?plain=1#L443 https://github.com/pllittle/CSeQTLworkflow/blob/df7e852100dbf2986e2dd84f8c8e928aa18e5a7e/README.md?plain=1#L503

I don't find Brain cell size data. It would be appreciated if the Brain cell size information could be shared.

Thanks in advanced!

Best, zhang