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Irrationone / cellassign

Automated, probabilistic assignment of cell types in scRNA-seq data
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How to perform cell-type assignments for clusters derived from unsupervised clustering? #62

Closed JingleW closed 4 years ago

JingleW commented 4 years ago

I want to use CellAssign to annotate my cells. I previously used Seurat to process my data and do unsupervised clustering. It seems there are two ways to use CellAssign and Seurat.

  1. Do unsupervised clustering with Seurat first, then subset each cluster and annotate it with CellAssign.
  2. Use CellAssign to annotate all the cells without unsupervised clustering firstly.

I wonder which method is right or is the best? Thanks a lot.

kieranrcampbell commented 4 years ago

Approach 2 is the correct way

On Mon, Dec 23, 2019 at 02:04 JingleW notifications@github.com wrote:

I want to use CellAssign to annotate my cells. I previously used Seurat to process my data and do unsupervised clustering. It seems there are two ways to use CellAssign and Seurat.

  1. Do unsupervised clustering with Seurat first, then subset each cluster and annotate it with CellAssign.
  2. Use CellAssign to annotate all the cells without unsupervised clustering firstly.

I wonder which method is right or is the best? Thanks a lot.

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