Awatramani Lab · Northwestern University

Dopaminergic neuron subtype classifier

Assign every cell in a raw sc/snRNA-seq dataset to one of 18 dopaminergic subtypes across the Sox6, Calb1 and Gad2 families, using the lab's hierarchical mixture-of-experts model.

18 subtypes, 3 families
.h5ad or Seurat .rds, raw counts
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Your data

Human (UPPER) or mouse (Title case) symbols both work. .rds can be a Seurat v3 or v5 object, a SingleCellExperiment, or a sparse count matrix.

Where are the raw counts?

adata.X adata.raw layers["counts"]

The gates were fit on raw UMI counts, so normalized or log-transformed values are rejected.

Exclude the Gad2 family

Reassign Gad2 calls to the best non-Gad2 subtype. Useful for TH+ or SLC6A3+ sorted data, where no GABAergic population is expected.

Preparing the classifier

Dopaminergic neuron subtype classifier

Your data

Results