annotation/workflows.csv

id,cell_type_workflow,niche_workflow
1,Annotated based on gene co-expression patterns.,NA
2,Leiden clustering with majority voting for consensus-based cell-type annotation; provided 3 tiers of annotation.,"Labeled niches from cell annotations with clear distributions (e.g. Atrium, Ventricular) for tier 1; considered spatial left/right position for tier 2."
3,Unknown.,"Unknown, likely mis-ordered annotations."
4,Leiden clustering and analyzed predefined marker genes in clusters; typically a single marker gene to differentiate cell types; projected cell types spatially and used position for final annotation.,Used UTAG for spatial clustering; labeled structures based on position and provided anatomical image.
5,Leiden clustering and analyzed expression of predefined marker genes in clusters; multiple genes per cell type; mapped both major cell type and subtypes.,"Used UTAG for spatial clustering; labeled structures based on position, provided anatomical image and additional sources."
6,"Label transfer using TACCO with an scRNA-seq reference of human heart; projected cell types spatially; Leiden clustering and DEG for marker genes, using key markers for second-tier annotation.",Used UTAG for spatial clustering; labeled structures based on position and provided anatomical image.
7,Leiden clustering with manual annotation using marker gene sets and DEG (per Scanpy tutorial); projected cell types spatially; used spatial position and key marker expression for final annotation; provided 3-tier annotation.,Used UTAG for spatial clustering; labeled structures based on position and anatomical knowledge of heart (e.g. 'chamber wall is thicker on the left ventricle').
8,Combined annotation on Leiden clusters with CellTypist-transferred labels as reference.,Used UTAG for spatial clustering.