single-cell-multi-omics-integration

single-cell-multi-omics-integration is a skill for Claude Code, Codex from omicverse/omicclaw. It costs 53 tokens per session (2,214 once invoked), scanned A, original, GPL-3.0.

A workflow for combining multiple kinds of biological measurements, such as single-cell RNA data and chromatin-accessibility data. It includes methods for finding shared patterns, aligning datasets, correcting batch differences, transferring cell labels, and tracing cell development over time.

In plain words
What is it for?
Use it to integrate paired or unpaired scRNA-seq and scATAC-seq data, identify hidden factors, correct batches, assign labels across datasets, and study cell trajectories.
Why use it?
It helps analyze datasets that measure different aspects of the same cells, including studies where the measurements were collected together or separately.

Skill for Claude CodeCodex

Which agent this was written for is unclear — body not stored (licence); the path alone says nothing.

Good fit Use it to integrate paired or unpaired scRNA-seq and scATAC-seq data, identify hidden factors, correct batches, assign labels across datasets, and study cell trajectories.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/omicverse/omicclaw/single-multiomics
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 omicverse/omicclaw --skill single-multiomics
Clone the repo
git clone --depth 1 https://github.com/omicverse/omicclaw

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 single-cell-multi-omics-integration

README.md
[![agentmods](https://agentmods.dev/badge/skills/omicverse/omicclaw/single-multiomics/github.svg)](https://agentmods.dev/skills/omicverse/omicclaw/single-multiomics)
Your own site
<a href="https://agentmods.dev/skills/omicverse/omicclaw/single-multiomics"><img src="https://agentmods.dev/badge/skills/omicverse/omicclaw/single-multiomics/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 single-cell-multi-omics-integration

Your own site · 80×15
<a href="https://agentmods.dev/skills/omicverse/omicclaw/single-multiomics"><img src="https://agentmods.dev/badge/skills/omicverse/omicclaw/single-multiomics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 53 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 2,214 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 unknown 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 $0.00053 $0.02214
Opus 5.5 $0.00021 $0.00886
Sonnet 5.5 $0.00011 $0.00443
Haiku 4.5 $0.00005 $0.00221

Measured 1mo ago against content hash 3efdbb0cc80c, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

single-cell-multi-omics-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 1mo ago.

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.

src/omicverse_skills/skills/single-multiomics/SKILL.md · 166 lines

The source is not reproduced here

Licensed GPL-3.0

The repository is licensed GPL-3.0, which this catalogue does not treat as permission to reproduce the file. Read it at the source.

Read it on GitHub

Files

What ships with it

1 file 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. 1mo ago First seen · 166 lines · 53 tokens per session scan A 3efdbb0cc80c

Subscribe to this mod's changes

single-cell-multi-omics-integration is a skill published in the GitHub repository omicverse/omicclaw (33 stars, last pushed 5mo ago), licensed GPL-3.0. It adds 53 tokens to every session and 2,214 once invoked, about $0.0002 per session on Opus 5.5. 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 2026-08-30.

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