Question: Best package to cluster a single cell dataset using marker gene lists retrieved from elsewhere?
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gravatar for A248
19 days ago by
A2480
A2480 wrote:

Say for example we have a PBMC single cell dataset generated in the lab, and would wish to use differentially expressed gene lists of different cell types (B, T, monocyte etc) which have been published elsewhere to guide the clustering of our single cell dataset.

Is there a package which would be best suited for this purpose?

Thanks

ADD COMMENTlink modified 19 days ago by jared.andrews074.1k • written 19 days ago by A2480
1
gravatar for jared.andrews07
19 days ago by
jared.andrews074.1k
St. Louis, MO
jared.andrews074.1k wrote:

I'm going to plug SingleR for this (full disclosure: I've been involved in its development). It will annotate your cells based on purified bulk or single-cell reference datasets, and it has several immune datasets built in that should easily handle PBMCs. It's also very easy to use and is work-flow agnostic - you can use it with pretty much any other packages (Seurat, scater, SingleCellExperiment, etc). As long as you have a count matrix, you can use it.

It's quick, it's easy, it has diagnostic visuals to ensure the results make sense, and it doesn't rely on users coming up with dependable marker sets themselves.

ADD COMMENTlink written 19 days ago by jared.andrews074.1k
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