Question: Best package to cluster a single cell dataset using marker gene lists retrieved from elsewhere?
gravatar for A248
3 months ago by
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?


ADD COMMENTlink modified 3 months ago by jared.andrews075.0k • written 3 months ago by A2480
gravatar for jared.andrews07
3 months ago by
St. Louis, MO
jared.andrews075.0k 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 3 months ago by jared.andrews075.0k
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