Question: Cell type assignment in single-cell RNAseq
1
gravatar for mBrio
3 months ago by
mBrio10
Münster
mBrio10 wrote:

Hi everybody,

I am dealing with the classification of different cell subpopulation in scRNA sequencing. Are there tools that automatically assign the identity of a cell cluster based on the differentially expressed genes? Any tool related would also be interesting to consider.

Thank you very much for your help!

Marta

ADD COMMENTlink modified 3 months ago by igor6.4k • written 3 months ago by mBrio10
1

I'm not sure I would trust a tool that much. There are so many poorly defined cell-types that it's probably still best to have experts look at the clusters.

ADD REPLYlink written 3 months ago by Devon Ryan81k
0
gravatar for dppb05
3 months ago by
dppb0550
dppb0550 wrote:

Monocle can do it to some extent, although it is not 100% automatic. The performance will depend on how well you define your filters (which will most likely depend on good markers for your data). Therefore you will still need to do some work (e.g. define good markers for your cell types).

ADD COMMENTlink written 3 months ago by dppb0550
0
gravatar for igor
3 months ago by
igor6.4k
United States
igor6.4k wrote:

This is actually more difficult than it may sound at first. There are a few suggestions in this previous thread: pathway for single cell RNA-seq

ADD COMMENTlink modified 3 months ago • written 3 months ago by igor6.4k
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