README.md

snapseed

Snapseed annotates single-cell datasets based on manually defined sets of marker genes for individual cell types or cell type hierarchies. It is fast and simple to accelerate annotation of very large datasets.

Quick start

import snapseed as snap
from snapseed.utils import read_yaml

# Read in the marker genes
marker_genes = read_yaml("marker_genes.yaml")

# Annotate anndata objects
snap.annotate(
    adata,
    marker_genes,
    group_name="clusters",
    layer="lognorm",
)

# Or for more complex hierarchies
snap.annotate_hierarchy(
    adata,
    marker_genes,
    group_name="clusters",
    layer="lognorm",
)