bulk analysis by seurat

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5.2 years ago

ayatrience • 0

Because seurat package is also technically available for bulk RNA-seq analysis and very easy to analyze for my bulk data with several conditions, I am trying to use Seurat for bulk analysis currently.

I use TPM countdata (rows are genes and cols are sample name) for CreateSeuratObject but gene names didn't appear in seurat object as features.

What kind of input is appropriate for making seurat object?

I have TPM count data and gene names in CSV format.

seurat RNA-Seq gene name • 3.7k views

ADD COMMENT • link 5.2 years ago by ayatrience • 0

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For questions like this, you really need to show all code that you have used, and paste a sample of your data.

ADD REPLY • link 5.2 years ago by Kevin Blighe 88k

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Thank you for teaching. I did like below.

bulk <- CreateSeuratObject(counts=TPM, assay = "RNA")

TPM is the list that contains the count data showed in TPM and the rows are genesID and cols are sample name.

ADD REPLY • link 5.2 years ago by ayatrience • 0

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I see - you likely need to use the meta.data parameter, too.

ADD REPLY • link 5.2 years ago by Kevin Blighe 88k

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Can you show more of your code and the first lines of your input ?

ADD REPLY • link 5.2 years ago by nlehmann ▴ 150

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