Question: Annotation of Single Cell Clusters
gravatar for Shelle
6 months ago by
Shelle0 wrote:

I am new to single cell. And I would appreciate guidance for my question

I want to cluster a given single cell dataset for example PBMC. How can I annotate different clusters in the single cell without the knowledge of biology? I came across the scanpy but it was not useful and sounded like you need to know the different type of marker genes beforehand.

Any help would be appreciated

ADD COMMENTlink modified 7 weeks ago by Ashwini Patil10 • written 6 months ago by Shelle0
gravatar for geek_y
6 months ago by
geek_y11k wrote:

One need to know cell-type marker genes to annotate the cell-types. As far as I know, no tool can do it without providing marker genes for cell-type.

ADD COMMENTlink written 6 months ago by geek_y11k

Is there any list of universal marker genes that I can use? For example for 7 clusters in one dataset how I can know which one is representing which cell type marker genes?

ADD REPLYlink modified 6 months ago • written 6 months ago by Shelle0

You have to provide markers based on the biology. Biology and analysis go hand-in-hand. If you have PBMCs then you can get markers from consortium datasets like Haemopedia or ImmGen. Check the singleR package which includes these datasets for hematopoietic cells and can assign identities to your clusters.

ADD REPLYlink written 6 months ago by ATpoint40k

Thanks for the information. Is there any other tool besides singleR which is not really dependent on Seurat? both of these tools are based on R and I would like to stay close to python because of downstream analysis

ADD REPLYlink written 6 months ago by Shelle0
gravatar for Ashwini Patil
7 weeks ago by
Japan/Tokyo/Combinatics Inc.
Ashwini Patil10 wrote:

Take a look at the CellKb database. You can enter a ranked gene list and get matching cell types previously published in literature through the web interface. Matching of the query gene list to other cell types is performed using a variation of the rank bias overlap algorithm. CellKb contains several marker gene sets for immune cell types, including those from SingleR, MSigDB and Human Protein Atlas.

Disclaimer: CellKb is a commercial product and I am involved in its development. Academic users can sign up for a free license and search limited single-cell datasets and all bulk datasets, including SingleR, MSigDB and Human Protein Atlas.

ADD COMMENTlink written 7 weeks ago by Ashwini Patil10
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