annotating single-cell clusters from gene lists

We're working on a scRNA-Seq data set, which I now want to annotate. Based on previous projects we have a list annotation categories in a tabular format.

From the examples I have seen, I need to have another Seurat or a singleCellExperiment object (or even, if using the celldex package a SummarizedExperiment object.) But all I have is a list of genes per category in a text file.

I was wondering how I can use a text file as an input to annotate my Seurat object I'm working on?

thanks
Assa

annotation findallmarkers seurat cell-type

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updated 2.4 years ago by Ram

• written 2.4 years ago by Assa Yeroslaviz

I use https://www.bioconductor.org/packages/release/bioc/html/UCell.htmlfor that.

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written 2.4 years ago by ATpoint

Thanks, I'll give it a try.

https://www.bioconductor.org/packages/release/bioc/html/UCell.html

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written 2.4 years ago by Assa Yeroslaviz

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