agentmods.dev

Omics Analysis Skills Index

Omics Analysis Skills Index is a skill for Claude Code, Codex from aristoteleo/PantheonOS. It costs 31 tokens per session (1,395 once invoked), scanned A, original, BSD-2-Clause.

An index of workflows for analyzing single-cell and spatial omics data, which measure biological molecules in individual cells or locations in tissue.

In plain words
What is it for?
Use it for quality control, doublet detection, normalization, cell-type labeling, trajectory analysis, RNA velocity, gene-panel design, and panel benchmarking.
Why use it?
It provides task-specific guidance for common analysis steps and for designing or evaluating gene panels instead of treating every omics project as the same.

Skill for Claude CodeCodex

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

not rated 484repo today A scan SkillSpector: pass 31 tokens original BSD-2-Clause

Good fit Use it for quality control, doublet detection, normalization, cell-type labeling, trajectory analysis, RNA velocity, gene-panel design, and panel benchmarking.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/aristoteleo/pantheonos/omics
View source ↗ aristoteleo/PantheonOS pantheonos.stanford.edu
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 aristoteleo/PantheonOS --skill omics
Clone the repo
git clone --depth 1 https://github.com/aristoteleo/PantheonOS

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 Omics Analysis Skills Index

README.md
[![agentmods](https://agentmods.dev/badge/skills/aristoteleo/pantheonos/omics/github.svg)](https://agentmods.dev/skills/aristoteleo/pantheonos/omics)
Your own site
<a href="https://agentmods.dev/skills/aristoteleo/pantheonos/omics"><img src="https://agentmods.dev/badge/skills/aristoteleo/pantheonos/omics/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 Omics Analysis Skills Index

Your own site · 80×15
<a href="https://agentmods.dev/skills/aristoteleo/pantheonos/omics"><img src="https://agentmods.dev/badge/skills/aristoteleo/pantheonos/omics.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 31 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 1,395 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. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
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 $0.00031 $0.01395
Opus 5 $0.00015 $0.00698
Sonnet 5 $0.00006 $0.00279
Haiku 4.5 $0.00003 $0.00139

Measured 9d ago against content hash 6799295e2ff1, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-08, from the pricing page.

Security

Grade A, and why

Omics Analysis Skills Index 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 9d ago.

The scan reads SKILL.md. This mod also ships 1 executable file (gene_panel_selection/scripts/gene_panel_helpers.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.

pantheon/factory/templates/skills/omics/SKILL.md · 161 lines

How it starts

The opening of the file, as written. The whole thing — 161 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Agent Skills for Omics Data Analysis

Best practices and workflows for single-cell and spatial omics analysis. Load the relevant skill files when performing specific analysis tasks.

Core Single-Cell Skills

High-priority, actionable workflows for the most common single-cell analysis tasks.

Skill index: single_cell/SKILL.md

Skills:

  • Quality Control: Filtering, doublet detection, normalization, QC metrics
  • Cell Type Annotation: Marker-based and reference-based label assignment
  • Trajectory Inference: Pseudotime, lineage tracing, RNA velocity

Gene Panel Selection

End-to-end workflow for designing gene panels in scRNA-seq and spatial transcriptomics (HVG/DE/RF/scGeneFit/SpaPROS), with sub-panel discovery, consensus scoring, biological completion, and benchmarking.

Skill folder: gene_panel_selection/

When to use:

  • Designing a gene panel for spatial transcriptomics in a static / terminal system
  • Benchmarking existing panels (ARI/NMI/Silhouette + UMAP)
  • IMPORTANT: When doing gene panel selection, strictly follow this workflow

Developmental Gene Panel Design

Panel design for developing / dynamic systems (embryonic organs, differentiation, regeneration), where terminal cell types are end-products of earlier lineage programs. Uses TWO references — the target (usually late) stage for cell-state resolution, and an independent EARLIER-stage reference mined by trajectory/pseudotime ranking for developmental regulators — under an explicit budget split.

Skill folder: developmental_gene_panel/

When to use (use this INSTEAD of gene_panel_selection):

  • The tissue is embryonic / differentiating / regenerating, or the user cares about lineage origin and regulators, not only terminal cell-type classification
  • The assay is at a late stage but the biology is a trajectory
  • Why it matters: developmental regulators are frequently NOT recoverable from the target stage — in a benchmarked case study six unbiased methods (cell-type DE, DPT pseudotime Pearson/Spearman, cross-stage ANOVA, global marker rank) all ranked a known CHD regulator in the top 0.6–1.8% on an early reference and failed (top 3–79%) on the target stage; literature lookup also failed

Read the full file on GitHub · 161 lines

Files

What ships with it

60 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. 9d ago First seen · 161 lines · 31 tokens per session scan A 6799295e2ff1

Subscribe to this mod's changes

Omics Analysis Skills Index is a skill published in the GitHub repository aristoteleo/PantheonOS (484 stars, last pushed today), licensed BSD-2-Clause. It adds 31 tokens to every session and 1,395 once invoked, about $0.0002 per session on Opus 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.

Data and AIScientificagentaiai-agentspantheonossinglecellspatial-transcriptomics
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