bio-workflows-multi-omics-pipeline
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and other modalities. Use when integrating multiple omics datasets.
npx skills add BioTender-max/awesome-bio-agent-skills --skill multi-omics-pipeline --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.
## Version Compatibility Reference examples tested with: clusterProfiler 4.10+, ggplot2 3.5+, scanpy 1.10+ Before using code patterns, verify installed versions match. If versions differ: - R: `packageVersion('<pkg>')` then `?function_name` to verify parameters If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Multi-omics Integration Pipeline **"Integrate my multi-omics datasets"** → Orchestrate data harmonization, MOFA+ factor analysis, mixOmics multivariate integration, similarity network fusion, and joint pathway interpretation across transcriptomics, proteomics, metabolomics, or other modalities. ## Pipeline Overview ``` RNA-seq Data ─────┐ │ Proteomics Data ──┼──> Data Harmonization ──> Integration ──> Factors/Components │ │ Metabolomics ─────┘ ▼ ┌─────────────────────────────────────────────────────┐ │ multi-omics-pipeline │ ├─────────────────────────────────────────────────────┤ │ 1. Data Preprocessing per Modality │ │ 2. Sample Harmonization (matching samples) │ │ 3. Feature Selection/Filtering │ │ 4. Integration (MOFA2 / mixOmics / SNF) │ │ 5. Factor/Component Int
- Version Compatibility
- Pipeline Overview
- Complete MOFA2 Workflow
- mixOmics DIABLO Workflow
- Similarity Network Fusion (SNF)
- QC Checkpoints
- Workflow Variants
- With Missing Samples
- Single-cell Multi-omics
- Related Skills
What does the bio-workflows-multi-omics-pipeline skill do?
End-to-end multi-omics integration workflow. Orchestrates data harmonization, MOFA/mixOmics integration, factor interpretation, and downstream analysis across transcriptomics, proteomics, metabolomics, and other modalities. Use when integrating multiple omics datasets.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill multi-omics-pipeline --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.