Single-Cell Analysis Skills Index
Core skills for single-cell RNA-seq analysis: quality control, cell type annotation, and trajectory inference. These are high-priority actionable workflows — load them first for common single-cell tasks.
npx skills add BioTender-max/awesome-bio-agent-skills --skill single_cell --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Core Single-Cell Analysis Skills High-priority, actionable workflows for the most common single-cell analysis tasks. For deeper background and alternative methods, see the supplementary [SC Best Practices](../sc_best_practices/SKILL.md) reference. ## Available Skills ### Quality Control Standard QC workflow: filtering low-quality cells, doublet detection, normalization, and QC metric visualization. **Skill file**: [quality_control.md](./quality_control.md) **When to use**: - Starting analysis of a new single-cell dataset - Need to filter low-quality cells - Assessing data quality metrics ### Cell Type Annotation Marker-based and reference-based approaches for assigning cell type labels. **Skill file**: [cell_type_annotation.md](./cell_type_annotation.md) **When to use**: - After clustering, need to assign cell type labels - Using marker genes for annotation - Using reference-based methods (CellTypist, scArches) ### Trajectory Inference Pseudotime analysis and trajectory inference for cell differentiation, lineage tracing, and RNA velocity. **Skill file**: [trajectory_inference.md](./trajectory_inference.md) **When to use**: - Studying cell differentiation paths - Neurogenesis or
- Available Skills
- Quality Control
- Cell Type Annotation
- Trajectory Inference
What does the Single-Cell Analysis Skills Index skill do?
Core skills for single-cell RNA-seq analysis: quality control, cell type annotation, and trajectory inference. These are high-priority actionable workflows — load them first for common single-cell tasks.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill single_cell --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.