What it is
Cell states (activation, exhaustion, ECM remodeling, antigen presentation, and similar programs) are resolved as distinct gene programs separate from the cell type label.
How to read it
The cell state field reports co-occurring functional programs. Multiple states can be active simultaneously. Each is supported by a specific gene set.
When to act
Unexpected states, such as exhaustion in naive T cells or proliferation in quiescent stromal cells, should prompt review of cluster composition. These are often the most biologically interesting signals.
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