FindAllMarkers, FindMarkers 以及 F

在seurat中，如果运行了RunUMAP或者RunTSNE后自动分群后，FindAllMarkers和FindMarkers基本就是一样的；如果没有进行RunUMAP或者RunTSNE分群，那么需要先运行BuildClusterTree(object)函数，利用树聚类先分群

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When use Seurat package to perform single-cell RNA seq, three functions are offered by constructors. They look similar but different anyway.
So I search around for discussion.

Here is original link

1. FindMarkers() will find markers between two different identity groups.
   You have to specify both identity groups. This is useful for comparing the differences between two specific groups.

2. FindAllMarkers() will find markers differentially expressed in each identity group by comparing it to all of the others.
   You don't have to manually define anything. Note that markers may bleed over between closely-related groups - they are not forced to be specific to only one group. This is what most people use (and likely what you want).

3. FindConservedMarkers() will find markers that are conserved between two groups.
   This can be useful if you want to find markers that are conserved between a treated and untreated condition for a specific cell type or group of cells. It means they are differentially expressed compared to other groups, but have similar expression between the two groups you're actually comparing.

大概就是说FindMarkers()是指定的两个组之间的差异基因；FindAllMarkers()是一个组和剩下其他组的差异基因，是最常用的；FindConservedMarkers()其实是在单细胞分析中，有两个处理组 'g1' 和 'g2' ，而 'g1' 和 'g2' 组中又恰好有相同的细胞亚群 0 和 1，求在 'g1' 中细胞亚群 0 和细胞亚群 1 的差异基因，并且与在 'g2' 中细胞亚群 0 和细胞亚群 1 的差异基因取交集；这部分基因定义为 在 'g1' 和 'g2' 组中，细胞亚群 0 和细胞亚群 1 差异保守的基因

转自：
FindAllMarkers, FindMarkers 以及 FindConservedMarkers 的区别 - 简书 (jianshu.com)
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat - 简书 (jianshu.com)