cellxgene-census

cellxgene-census is a skill for Claude Code from jimmc414/Kosmos. It costs 47 tokens per session (3,721 once invoked), scanned A, original, no licence file.

A tool for querying CZ CELLxGENE Census, a large collection of single-cell gene-expression data. Single-cell analysis measures genes in individual cells rather than only across whole tissue samples.

In plain words
What is it for?
Use it to filter and retrieve expression data by cell type, tissue, or disease, and use the results with Scanpy or PyTorch.
Why use it?
It avoids downloading and filtering the entire collection when only certain cell types, tissues, or diseases are needed.

Skill for Claude Code

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

Part of the scientific-skills plugin — 119 skills shipped together

Good fit Use it to filter and retrieve expression data by cell type, tissue, or disease, and use the results with Scanpy or PyTorch.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jimmc414/kosmos/cellxgene-census
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 jimmc414/Kosmos --skill cellxgene-census
Clone the repo
git clone --depth 1 https://github.com/jimmc414/Kosmos

Made for: Claude Code.

Or install scientific-skills, the plugin that ships this one along with the rest of its 119 skills.

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-census

README.md
[![agentmods](https://agentmods.dev/badge/skills/jimmc414/kosmos/cellxgene-census/github.svg)](https://agentmods.dev/skills/jimmc414/kosmos/cellxgene-census)
Your own site
<a href="https://agentmods.dev/skills/jimmc414/kosmos/cellxgene-census"><img src="https://agentmods.dev/badge/skills/jimmc414/kosmos/cellxgene-census/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-census

Your own site · 80×15
<a href="https://agentmods.dev/skills/jimmc414/kosmos/cellxgene-census"><img src="https://agentmods.dev/badge/skills/jimmc414/kosmos/cellxgene-census.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 47 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 3,721 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 $0.00047 $0.03721
Opus 5 $0.00023 $0.01861
Sonnet 5 $0.00009 $0.00744
Haiku 4.5 $0.00005 $0.00372

Measured 10d ago against content hash eb3ab532d018, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

cellxgene-census 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 10d 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.

kosmos-claude-scientific-skills/scientific-skills/cellxgene-census/SKILL.md · 506 lines

The source is not reproduced here

No licence file

A repository with no LICENSE is all rights reserved by default, so the body is not copied here. The metadata, the measurements and the link are.

Read it on GitHub

Files

What ships with it

2 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. 10d ago First seen · 506 lines · 47 tokens per session scan A eb3ab532d018

Subscribe to this mod's changes

cellxgene-census is a skill published in the GitHub repository jimmc414/Kosmos (582 stars, last pushed 5mo ago), with no licence file. It adds 47 tokens to every session and 3,721 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.

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