# 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.

- Skill: `gabrielmoreira/single-cell-analysis-skills-index` (Agent Skill, multi-file: 4 files)
- Install (CLI): `npx skillmds@latest add gabrielmoreira/single-cell-analysis-skills-index`
- Raw SKILL.md: https://api.skillmd.com/api/skills/gabrielmoreira/single-cell-analysis-skills-index/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: AI & ML
- Author: gabrielmoreira (https://skillmd.com/u/gabrielmoreira)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/gabrielmoreira/single-cell-analysis-skills-index

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# 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 developmental trajectory analysis
- RNA velocity for directional dynamics