cellxgene-context

cellxgene-context is a skill for Claude Code from ammawla/encode-toolkit. It costs 86 tokens per session (5,050 once invoked), scanned A, original, AGPL-3.0.

A guide for combining CellxGene Census, a large single-cell gene-expression database, with ENCODE, a public collection of regulatory genomics experiments. It adds cell-type context to bulk measurements.

In plain words
What is it for?
Use it to study cell-type-specific expression, separate mixed ENCODE signals by cell type, and check regulatory elements against single-cell evidence.
Why use it?
Bulk experiments mix signals from many cell types, making it hard to tell which cells drive a result. This guide helps compare those signals with single-cell data.

Skill for Claude Code

Written for Claude Code: shipped in a Claude Code plugin.

Part of the encode-toolkit plugin — 47 skills, 1 MCP server shipped together

Good fit Use it to study cell-type-specific expression, separate mixed ENCODE signals by cell type, and check regulatory elements against single-cell evidence.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/ammawla/encode-toolkit/cellxgene-context
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 ammawla/encode-toolkit --skill cellxgene-context
Clone the repo
git clone --depth 1 https://github.com/ammawla/encode-toolkit

Made for: Claude Code.

Or install encode-toolkit, the plugin that ships this one along with the rest of its 47 skills, 1 MCP server.

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 cellxgene-context

README.md
[![agentmods](https://agentmods.dev/badge/skills/ammawla/encode-toolkit/cellxgene-context/github.svg)](https://agentmods.dev/skills/ammawla/encode-toolkit/cellxgene-context)
Your own site
<a href="https://agentmods.dev/skills/ammawla/encode-toolkit/cellxgene-context"><img src="https://agentmods.dev/badge/skills/ammawla/encode-toolkit/cellxgene-context/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 cellxgene-context

Your own site · 80×15
<a href="https://agentmods.dev/skills/ammawla/encode-toolkit/cellxgene-context"><img src="https://agentmods.dev/badge/skills/ammawla/encode-toolkit/cellxgene-context.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 86 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 5,050 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 $0.00086 $0.05050
Opus 5.5 $0.00034 $0.02020
Sonnet 5.5 $0.00017 $0.01010
Haiku 4.5 $0.00009 $0.00505

Measured 1mo ago against content hash 7086b6a93e84, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

cellxgene-context 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.

plugin/skills/cellxgene-context/SKILL.md · 471 lines

The source is not reproduced here

Licensed AGPL-3.0

The repository is licensed AGPL-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 Changed · +27 lines 7086b6a93e84
  2. 1mo ago First seen · 444 lines · 86 tokens per session scan A 3953cc0c269c

Subscribe to this mod's changes

cellxgene-context is a skill published in the GitHub repository ammawla/encode-toolkit (21 stars, last pushed 26d ago), licensed AGPL-3.0. It adds 86 tokens to every session and 5,050 once invoked, about $0.0003 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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