How to see all gene expressions in all clusters in scRNA-seq?

[CicySue]

Hey, I'm stuck in this step. After UMAP, I don't know how to see all gene expressions in all clusters. All tutorials from websites are all telling you how to find marker genes in every cluster. But I want to get a file of the expression of all genes in all clusters. And ideally the row names are genes and the column names are clusters.

[mbm2224]

Have you tried aggregating gene expression? You can try using this function, and then writing out the count matrix as a csv or mtx file. If the idents are clusters, then it will aggregate cells to cluster, so clusters will be column and genes are rows.

Out of curiosity, may I ask why you want this information and what you plan to do with it?

[CicySue]

thank u sooooooo much! Because we want to see the difference among clusters, but the heatmap didn’t do a god job cause it’s too messy mbm2224 ***@***.***>于2023年7月11日 周二09:48写道：

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Have you tried aggregating gene expression? You can try using this function <https://satijalab.org/seurat/reference/aggregateexpression>, and then writing out the count matrix as a csv or mtx file. If the idents are clusters, then it will aggregate cells to cluster, so clusters will be column and genes are rows. Out of curiosity, may I ask why you want this information and what you plan to do with it? — Reply to this email directly, view it on GitHub <#7544 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BBFB46DFMUERIPBNYABEKX3XPVKR3ANCNFSM6AAAAAA2DV3PDM> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>