Topic
Marker gene sanity
Are my cluster markers real cell identity or ribosomal, mitochondrial and stress genes?
FindMarkers returns the genes most different between one cluster and the rest, which is often a dissociation-stress signature, a cell-cycle phase or a sequencing-depth artifact. A marker is only trustworthy if it is specific, expressed in most cells of the cluster, and matches literature you can cite.
- How to Sanity-Check Marker Genes and Cell Type Labels in Single-Cell ATAC-seq
A marker with a huge fold-change can still be sequencing depth or dissociation stress in disguise, here's how to tell before you write the label on the UMAP.
- How to Sanity-Check Marker Genes and Cell Type Labels in Single-Cell RNA-seq
A FindMarkers table full of RPL, RPS, MT- and FOS genes isn't a cell type. Here's how to catch it before the label ships.
- How to Sanity-Check Marker Genes and Cell Type Labels in Single-Nucleus RNA-seq
FindMarkers will happily hand you a stress signature, an ambient RNA gradient, or a pseudoreplication artifact and let you name a cluster after it.
- How to Sanity-Check Marker Genes and Cell Type Labels in Spatial Transcriptomics
FindMarkers and rank_genes_groups will happily hand you ribosomal genes and dissociation stress as your top "cell type marker", here is the checklist that catches it before it reaches a figure legend.