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BI
bio-multi-omics-mixomics-analysis
Maintainer FreedomIntelligence · Last updated April 1, 2026
Supervised and unsupervised multi-omics integration with mixOmics. Includes sPLS for pairwise integration and DIABLO for multi-block discriminant analysis. Use when performing supervised multi-omics integration or identifying features that discriminate between groups.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-multi-omics-mixomics-analysis
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- R: mixOmics::block.splsda() (DIABLO), mixOmics::spls() for pairwise integration.
- Integrate my multi-omics data with supervised analysis" → Identify cross-omics feature signatures that discriminate between groups using sparse PLS and multi-block discriminant analysis. R: mixOmics::block.splsda() (DIABLO), mixOmics::spls() for pairwise integration.
- X_rna <- as.matrix(read.csv('rnaseq.csv', row.names = 1)) X_protein <- as.matrix(read.csv('proteomics.csv', row.names = 1)) Y <- factor(read.csv('phenotype.csv')$Condition).
Source Doc
Excerpt From SKILL.md
Setup and Data Preparation
Goal: Load and align omics matrices with matching sample labels and phenotype information.
Approach: Read each omics layer and phenotype, then intersect to common samples.
library(mixOmics)
## Ensure matching samples
common <- Reduce(intersect, list(rownames(X_rna), rownames(X_protein)))
X_rna <- X_rna[common, ]
X_protein <- X_protein[common, ]
Y <- Y[match(common, read.csv('phenotype.csv')$Sample)]
Pairwise Integration: sPLS
Goal: Identify correlated features between two omics layers using sparse partial least squares.
Approach: Tune component count, fit sPLS with feature selection (keepX/keepY), and visualize cross-omics correlations.
Use cases
- Use when performing supervised multi-omics integration or identifying features that discriminate between groups.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
Upstream Related Skills
- mofa-integration - Unsupervised multi-omics
- data-harmonization - Preprocess before integration
- differential-expression/de-results - Single-omics analysis
- pathway-analysis/go-enrichment - Interpret selected features
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