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multiomics-integration

multiomics-integration is a skill for Claude Code, Codex from zamushwani/biomedical-ai-skills. It costs 0 tokens per session (4,146 once invoked), scanned A, original, MIT.

A set of methods for analysing several kinds of molecular data from the same samples, such as gene activity, DNA changes, methylation, or protein levels. It can combine these data to find shared patterns or build predictive models.

In plain words
What is it for?
Use it to combine molecular datasets, identify cancer subtypes, find shared underlying factors, make supervised predictions, and model survival using integrated features.
Why use it?
It helps choose a suitable integration method and handle differences in scale, missing values, and preprocessing between data types. This makes combined analyses less likely to be distorted by one data layer.

Skill for Claude CodeCodex

Written for no agent in particular: nothing here depends on one.

not rated 1repo 1mo ago A scan 0 tokens original MIT

Good fit Use it to combine molecular datasets, identify cancer subtypes, find shared underlying factors, make supervised predictions, and model survival using integrated features.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/zamushwani/biomedical-ai-skills/multiomics-integration
View source ↗ zamushwani/biomedical-ai-skills
Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent
npx skills add zamushwani/biomedical-ai-skills --skill multiomics-integration
Clone the repo
git clone --depth 1 https://github.com/zamushwani/biomedical-ai-skills

Made for: Claude Code, Codex.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

agentmods badge for multiomics-integration

README.md
[![agentmods](https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/multiomics-integration/github.svg)](https://agentmods.dev/skills/zamushwani/biomedical-ai-skills/multiomics-integration)
Your own site
<a href="https://agentmods.dev/skills/zamushwani/biomedical-ai-skills/multiomics-integration"><img src="https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/multiomics-integration/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

agentmods 80×15 button for multiomics-integration

Your own site · 80×15
<a href="https://agentmods.dev/skills/zamushwani/biomedical-ai-skills/multiomics-integration"><img src="https://agentmods.dev/badge/skills/zamushwani/biomedical-ai-skills/multiomics-integration.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 0 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 4,146 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe.
Origin original No closer match found in the catalogue.
Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

ModelPer sessionOnce invoked
Fable 5.1 $0.00000 $0.04146
Opus 5.5 $0.00000 $0.01658
Sonnet 5.5 $0.00000 $0.00829
Haiku 4.5 $0.00000 $0.00415

Measured 2mo ago against content hash 3538485e1395, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

multiomics-integration scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.

The scan reads SKILL.md. This mod also ships 2 executable files (tests/run_all.py, tests/validate_packages.py), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/multiomics-integration/SKILL.md · 384 lines

How it starts

The opening of the file, as written. The whole thing — 384 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Multi-Omics Integration

Joint analysis of two or more molecular layers on the same samples. Covers method selection, the preprocessing that decides whether integration works at all, MOFA+ factor analysis, similarity network fusion, joint clustering for cancer subtyping, supervised integration, and survival models built on integrated features.

When to Use This Skill

Activate when the user requests:

  • Combining expression with methylation, mutation, CNV, or proteomics
  • MOFA+, MOFA2, SNF, iClusterPlus, DIABLO, or mixOmics
  • Cancer subtyping from more than one data type
  • Latent factors or components shared across omics layers
  • Survival modelling on integrated multi-omics features
  • Deciding which integration method suits their design

Inputs

Data Type Form Note
Expression genes x samples, log-CPM or VST usually the largest view
Methylation probes/regions x samples, M-values beta-values are heteroscedastic
CNV segments or gene-level x samples discrete-ish, often bimodal
Proteomics proteins x samples far fewer features, more missingness
Clinical samples x variables outcome for supervised methods

Every view must be indexed by the same sample identifiers. Integration is a join before it is a model.

Environment

Versions verified 2026-08.

BiocManager::install("MOFA2")           # 1.22.0  factor analysis
BiocManager::install("iClusterPlus")    # 1.48.0  joint clustering
BiocManager::install("mixOmics")        # 6.36.0  supervised (DIABLO)
install.packages("SNFtool")             # 2.3.1   similarity fusion

INSTALL mixOmics FROM BIOCONDUCTOR, NOT CRAN.

  CRAN         mixOmics 6.3.2, published 2018-06-01
  Bioconductor mixOmics 6.36.0

install.packages("mixOmics") silently gives you an eight-year-old build with
a different API. This is the same trap as PharmacoGx. Check which one you
actually loaded: packageVersion("mixOmics").

SNFtool 2.3.1 was last released 2021-06-11. It still works and the algorithm
is unchanged, but expect no fixes. Say so when you depend on it.

Read the full file on GitHub · 384 lines

Files

What ships with it

4 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

  1. 2mo ago First seen · 384 lines · 0 tokens per session scan A 3538485e1395

Subscribe to this mod's changes

multiomics-integration is a skill published in the GitHub repository zamushwani/biomedical-ai-skills (1 stars, last pushed 1mo ago), licensed MIT. It costs nothing until one of its globs matches a file; then it loads 4,146 tokens. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.

DESeq2Data and AIScientificai-agentai-skillsbioinformaticscancer-genomicscancer-research
Related

multiomics-integration compared with skills from other repositories

multiomics-integration next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
multiomics-integrationzamushwani/biomedical-ai-skillsSkill11mo agoMITA0Claude Code, Codex
cerna-analysisaipoch/medical-research-skillsSkill2.0k1mo agoMITA68Claude Code, Codex
cibersort-immune-infiltration-analysisaipoch/medical-research-skillsSkill2.0k1mo agoMITA92Claude Code, Codex
gene-protein-expression-matrix-normalizationaipoch/medical-research-skillsSkill2.0k1mo agoMITA63Claude Code, Codex
genomic-intelligenceK-Dense-AI/scientific-agent-skillsSkill56k5d agoMITA151Claude Code, Codex
torch-geometricK-Dense-AI/scientific-agent-skillsSkill56k5d agoMITA71Claude Code, Codex
bidsK-Dense-AI/scientific-agent-skillsSkill56k5d agoMITA84Claude Code, Codex