Imputation of scRNA-seq data

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4.8 years ago

mariafirulevabio ▴ 40

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.

scRNA-seq imputation RNA-Seq • 1.7k views

ADD COMMENT • link 4.8 years ago by mariafirulevabio ▴ 40

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

ADD REPLY • link 4.8 years ago by jared.andrews07 ★ 16k

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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 REPLY • link 4.8 years ago by igor 13k

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