Omics Analysis Skills Index
Skills for single-cell and spatial omics data analysis. Best practices, code snippets, and workflows for the scverse ecosystem.
npx skills add BioTender-max/awesome-bio-agent-skills --skill omics --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.
# Agent Skills for Omics Data Analysis Best practices and workflows for single-cell and spatial omics analysis. Load the relevant skill files when performing specific analysis tasks. ## Core Single-Cell Skills High-priority, actionable workflows for the most common single-cell analysis tasks. **Skill index**: [single_cell/SKILL.md](./single_cell/SKILL.md) **Skills**: - **Quality Control**: Filtering, doublet detection, normalization, QC metrics - **Cell Type Annotation**: Marker-based and reference-based label assignment - **Trajectory Inference**: Pseudotime, lineage tracing, RNA velocity --- ## Gene Panel Selection End-to-end workflow for designing gene panels in scRNA-seq and spatial transcriptomics (HVG/DE/RF/scGeneFit/SpaPROS), with sub-panel discovery, consensus scoring, biological completion, and benchmarking. **Skill folder**: [gene_panel_selection/](./gene_panel_selection/) **When to use**: - Designing a gene panel for spatial transcriptomics - Benchmarking existing panels (ARI/NMI/Silhouette + UMAP) - **IMPORTANT**: When doing gene panel selection, **strictly** follow this workflow --- ## Spatial Omics Skills for spatial transcriptomics mapping, imputation, and 3D visuali
- Core Single-Cell Skills
- Gene Panel Selection
- Spatial Omics
- Single-Cell Foundation Models (SCFM)
- Database Access
- Upstream Processing
- General Data Analysis
- Supplementary Reference: SC Best Practices
- Using Skills
What does the Omics Analysis Skills Index skill do?
Skills for single-cell and spatial omics data analysis. Best practices, code snippets, and workflows for the scverse ecosystem.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill omics --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.