Cell type assignment in single-cell RNAseq

Question

[mBrio]

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

[Devon Ryan]

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.

Answer 1

[dppb05]

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).

Answer 2

[igor]

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