Annotate osteosarcoma samples across ScPCA

[sjspielman]

Proposed analysis

The Data Lab plans to annotate all osteosarcoma samples in the ScPCA portal. Although this is across several projects, all annotation will be performed in a single analysis module since the procedure will be identical for all of them.

We will use the OsteoCAR reference for annotation, selecting the appropriate reference (either human primary, human metastatis, or PDX) for each sample.

We will follow a similar procedure to that adopted for the cell-type-neuroblastoma-04 module:

• Perform cell type annotation with SingleR
• Perform cell type annotation with scANVI
• Combine these results with consensus annotations to derive a final set of annotations based on a set of rules to be determined by forthcoming results

Scientific goals

Add cell types to osteo samples

Methods or approach

SingleR and scANVI

Existing modules

No other modules will be used, but much code will be inspired by the cell-type-neuroblastoma-04 module.

Input data

Projects SCPCP0000{17,18,23}

Scientific literature

See the osteocar paper: https://www.biorxiv.org/content/10.64898/2026.01.13.698472v3

Other details

No response