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single-cell-annotation-guide

single-cell-annotation-guide is a skill for Claude Code from jaechang-hits/SciAgent-Skills. It costs 75 tokens per session (7,523 once invoked), scanned A, original, no licence file.

A guide for deciding how to label cell types in single-cell RNA sequencing data. It compares manual marker-gene checks with automated tools and reference-based methods.

In plain words
What is it for?
Use it when planning or reviewing cell-type annotation, from checking known marker genes to using CellTypist or reference-based population transfer.
Why use it?
Cell-type labels can be uncertain, especially when cell states overlap or the reference data is imperfect. The guide helps choose an annotation method and troubleshoot disagreements.

Skill for Claude Code

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

Part of the sciagent-skills plugin — 206 skills shipped together

not rated 384repo +1 changed 1mo ago A scan 75 tokens custom licence

Good fit Use it when planning or reviewing cell-type annotation, from checking known marker genes to using CellTypist or reference-based population transfer.

Compare 6 skills from other repositories ↓
Install with agentmods
npx agentmods add skills/jaechang-hits/sciagent-skills/single-cell-annotation-guide
View source ↗ jaechang-hits/SciAgent-Skills omicshorizon.ai
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 jaechang-hits/SciAgent-Skills --skill single-cell-annotation-guide
Clone the repo
git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills

Made for: Claude Code.

Or install sciagent-skills, the plugin that ships this one along with the rest of its 206 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 single-cell-annotation-guide

README.md
[![agentmods](https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/single-cell-annotation-guide/github.svg)](https://agentmods.dev/skills/jaechang-hits/sciagent-skills/single-cell-annotation-guide)
Your own site
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/single-cell-annotation-guide"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/single-cell-annotation-guide/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-annotation-guide

Your own site · 80×15
<a href="https://agentmods.dev/skills/jaechang-hits/sciagent-skills/single-cell-annotation-guide"><img src="https://agentmods.dev/badge/skills/jaechang-hits/sciagent-skills/single-cell-annotation-guide.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 75 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 7,523 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 $0.00075 $0.07523
Opus 5.5 $0.00030 $0.03009
Sonnet 5.5 $0.00015 $0.01505
Haiku 4.5 $0.00007 $0.00752

Measured 1mo ago against content hash d34a2cb44331, 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-annotation-guide 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.

skills/genomics-bioinformatics/single-cell/single-cell-annotation-guide/SKILL.md · 338 lines

The source is not reproduced here

A licence we could not identify

The repository carries a LICENSE file, but it is custom or dual enough that GitHub cannot name it and neither can this catalogue. Unknown terms are not permission, so the body is not copied here. Read the licence at the source and decide for yourself.

Read it on GitHub

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 · +86 lines · +8 tokens per session d34a2cb44331
  2. 2mo ago First seen · 252 lines · 67 tokens per session scan A d9825d8ad1a1

Subscribe to this mod's changes

single-cell-annotation-guide is a skill published in the GitHub repository jaechang-hits/SciAgent-Skills (384 stars, last pushed 2d ago), with no licence file. It adds 75 tokens to every session and 7,523 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 2026-09-03.

Claude CodePlanningScientificai-agentbioinformaticsclaude-plugindrug-discoverygenomics
Related

single-cell-annotation-guide compared with skills from other repositories

single-cell-annotation-guide next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
single-cell-annotation-guidejaechang-hits/SciAgent-SkillsSkill3842d agononeA75Claude Code
bioinformatics-on-healthomicsawslabs/hcls-agent-skillsSkill721mo agoMIT-0A199Claude Code, Codex
biomcp-researchgenomoncology/biomcpSkill674yesterdayMITA36Claude Code
drug-discovery-searchbeita6969/ScienceClawSkill1.0kyesterdayMITB33Claude Code, Codex
genomics-alignmentTianGzlab/OmicsClawSkill1611mo agoApache-2.0A89Claude Code, Codex
genomics-cnv-callingTianGzlab/OmicsClawSkill1611mo agoApache-2.0A95Claude Code, Codex
genomics-epigenomicsTianGzlab/OmicsClawSkill1611mo agoApache-2.0A79Claude Code, Codex