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.
--> snapseed is now integrated into HNOCA-tools
importsnapseedassnapfromsnapseed.utilsimportread_yaml# Read in the marker genesmarker_genes=read_yaml("marker_genes.yaml")
# Annotate anndata objectssnap.annotate(
adata,
marker_genes,
group_name="clusters",
layer="lognorm",
)
# Or for more complex hierarchiessnap.annotate_hierarchy(
adata,
marker_genes,
group_name="clusters",
layer="lognorm",
)