Single-cell Analysis
Single-cell analysis
Explore cell-level expression and annotation while retaining the sample-level biological context.
Questions to discuss
- What cell populations and expression patterns are represented?
- Which quality or technical effects should be investigated?
- What evidence supports each proposed cell annotation?
Input for review
- Count matrices or processed objects for review, with processing history and cell/gene identifiers.
- Sample and donor identifiers, condition, platform, chemistry and batch information.
- Organism, assay and annotation references; raw versus filtered matrix status.
Analysis planning
- Review sample provenance, filtering decisions and quality distributions.
- Assess doublets and integration requirements as appropriate.
- Explore neighborhoods, embeddings, clusters and marker expression.
- Review annotation evidence and define donor-aware comparisons if feasible.
Reporting options
- Cell and sample QC summaries, embeddings and cluster summaries.
- Marker tables and annotation evidence.
- Processed objects and documented settings when included in the scope.
Interpretation
An embedding summarizes patterns and is exploratory. Cell counts do not substitute for independent donors or biological samples in condition-level inference.