Question: Imputation of scRNA-seq data
gravatar for mariafirulevabio
12 months ago by
mariafirulevabio40 wrote:

There are several tools for imputation of scRNA-seq data, most of them have released in 2018-2019. Since these programs were announced recently, it is complicated to find info about user' choice, except several articles for comparison several of these tools (e.g., this). Will you provide me your background about this point if you familiar with scRNA-seq and use imputation algorithms for your data? Also, I found AddImputedScore function in old Seurat version, but there is no information about AddImputedScore in Seurat v3.

rna-seq imputation scrna-seq • 531 views
ADD COMMENTlink written 12 months ago by mariafirulevabio40

For Seurat, you want the RunALRA function. I've never used it, but I think that replaced the old AddImputedScore function.

ADD REPLYlink written 12 months ago by jared.andrews076.2k

All the methods I have seen just take the counts matrix. I am not sure the Seurat integration is really necessary or helpful since it's one line to export/import the input/output matrix.

ADD REPLYlink written 12 months ago by igor11k
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