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 majiayu000/claude-skill-registry --skill multi-omics-pipeline-gptomics-bioskills-2 --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.
# Multi-omics Integration Pipeline ## 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 Interpretation │ │ 6. Downstream Analysis │ └─────────────────────────────────────────────────────┘ │ ▼ Integrated Factors + Biomarker Signatures ``` ## Complete MOFA2 Workflow ```r library(MOFA2) library(MOFAdata) library(ggplot2) library(tidyverse) # === 1. LOAD AND HARMONIZE DATA === # RNA-seq data (samples x genes) rna <- read.csv('rnaseq_normalized.csv', row.names = 1) cat('RNA:', nrow(rna), 'samples,', ncol(rna), 'genes\n') # Proteomics data (samples x proteins) protein <- read.csv('proteomics_normalized.csv', row.names = 1) cat('Protein:', nrow(protein), 'samples,', ncol(protein), 'proteins\n') # Metabolomics data (samples x metabolites) metab <- read.csv('metabolomics_no
- 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 majiayu000/claude-skill-registry --skill multi-omics-pipeline-gptomics-bioskills-2 --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 majiayu000/claude-skill-registry, a repository with 534 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.