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sulab-wmu / scPagwas

Obtain trait-relevant cell subpopulations by incorporating pathway activity transformed scRNA-seq data with GWAS data
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Does this apply to animals #23

Open zywz12138 opened 8 months ago

zywz12138 commented 8 months ago

请问把相关的文件（如：pathway，chrom_LD等）替换成动物的，是否就可以用这个软件在动物上进行gwas和单细胞的整合分析？

dengchunyu commented 8 months ago

可以，同时把block_annotation，Genes_by_pathway_kegg，chrom_ld替换成动物的

auesro commented 2 months ago

Hi, I would like to use scPagwas combining GWAS data from human and scRNAseq data from mouse. What would be the steps? If I change the block_annotation，Genes_by_pathway_kegg，chrom_ld files to contain mouse genes but the GWAS is human...it will not work, right?

Thanks!

dengchunyu commented 2 months ago

是的

Augusto Escalante @.***> 于2024年6月21日周五 22:35写道：

Hi, I would like to use scPagwas combining GWAS data from human and scRNAseq data from mouse. What would be the steps? If I change the block_annotation，Genes_by_pathway_kegg，chrom_ld files to contain mouse genes but the GWAS is human...it will not work, right?

Thanks!

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auesro commented 2 months ago

Hi @dengchunyu ,

What do you mean?

dengchunyu commented 2 months ago

Human GWAS data only apply to human single cells and cannot be extended to mouse data. Similarly, matching pathway data is not appropriate for this purpose.

Augusto Escalante @.***> 于2024年6月26日周三 14:54写道：

Hi @dengchunyu https://github.com/dengchunyu ,

What do you mean?

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auesro commented 2 months ago

Thank you for the clarification @dengchunyu Then there is no way to use scPagwas with scRNAseq animal data?

dengchunyu commented 2 months ago

If human data is unavailable, single-cell data from mice can be utilized for assistance.

Augusto Escalante @.***> 于2024年6月26日周三 15:38写道：

Thank you for the clarification @dengchunyu https://github.com/dengchunyu Then there is no way to use scPagwas with scRNAseq animal data?

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auesro commented 2 months ago

Ok, how can you do that? How did you do it for the mouse AD data in the paper?