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siya-kk / POP

Single-cell transcriptome profiling of the vaginal wall in women with severe anterior vaginal prolapse
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如何进行SCENIC分析？ #2

Open Dongxu-Zheng opened 3 years ago

Dongxu-Zheng commented 3 years ago

你好，我对文章中关于SCENIC的分析过程很感兴趣，但是根据文章的描述，不太确定我的理解是否正确。 根据文章内容，分析的第一步是单独使用正常样品的raw count进行SCENIC分析，预测了每个细胞类型特异的TFs，随后依次把每个来自疾病样本的细胞类型的raw count进行SCENI分析。不知道我的理解是否准确？希望能得到答复，非常感谢！

siya-kk commented 3 years ago

Hello Dongxu, For the SCENIC analysis, the normal sample and POP sample are separate, as same as the diff cells.

Dongxu-Zheng commented 3 years ago

So fisrt you input raw count matrix(all of the celltypes) of POP and normal samples separately to SCENIC to predict TFs/Regulons. Then you performed the same analysis on raw count matrix of each celltype under different conditions(Normal and POP) based on the code you upload here. Is that correct? I was wondering how to use SCENIC to compare samples from different conditions. The group of SCENIC suggested just input the integrated data including normal and disease to SCENIC and then compare activity score under different conditions.

Thanks in advance.