I’m trying to identify marker genes for each cell cluster in “multiple cortical areas” snRNA data sets,
It would be great if you could help me with the following questions:
What was the algorithm for selecting this list of “marker genes” in Transcriptomics Explorer :: Allen Brain Atlas: Cell Types?
Does the “marker genes” provided on the y-axis include all markers of the cell-specific clusters?
2.1. If yes, then are the marker genes for each cell-specific cluster those genes with non-zero expression values in the heat-map?
2.2. And if the y-axis does not include all the cell-specific marker genes, then is there a way you could suggest for extracting a complete set of marker genes? such as thresholding or filtering the trimmed means of gene expression in each cell-specific cluster?
Why are the cell-specific marker genes in multiple cortical areas dataset -provided by Cytosplore- different from those provided by the transcriptomic explorer?
How can I extract the cell-specific gene sets (rather than marker genes) for each cluster?
I appreciate your help,