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
2 answers
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).
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
Log in to answer this question.
-
single-cell differential expression of unbalanced cell number
written by Yingying •
-
GSVA with a genelist on a "per-cluster" basis
written by bio_info •
-
Allele specific expression of imprinted gens from 10x scRNA-seq data
written by singcell •
-
How can one determine if a sample size is representative in scRNA-seq analysis?
written by fifty_fifty •
-
Neuronal markers are expressed in all cell types in 10X single-cell RNASeq
written by viktorfeketa •
-
Manual annotation of cell types in single cell RNA-seq
written by Gene_MMP8
-
FindConservedMarkers vs FindMarkers vs FindAllMarkers Seurat
written by Payal
-
Cell lineage identification from pathway anlaysis
written by rob.costa1234
-
How to cluster differential expressed genes from RNA-seq analysis?
written by Kurban
-
K-means clustering of differentially expressed genes based on GO
written by Atefeh Mahdavi •
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.