Alphagenome Single Variant Analysis
google-deepmind/science-skills
Analyzes genetic variant effects on gene expression (RNA-seq), chromatin accessibility (DNASE), histone marks (ChIP), and transcription factors using the AlphaGenome API.
Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
Install Single Cell Annotation
$ npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills single-cell-annotation --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/legacy/single-cell-annotation .claude/skills/single-cell-annotation && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "single-cell-annotation" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation into .claude/skills/single-cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotationType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills single-cell-annotation --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/legacy/single-cell-annotation .agents/skills/single-cell-annotation && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "single-cell-annotation" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation into .agents/skills/single-cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills single-cell-annotation --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/legacy/single-cell-annotation .cursor/skills/single-cell-annotation && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "single-cell-annotation" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation into .cursor/skills/single-cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/jaechang-hits/SciAgent-Skills.git --path legacy/single-cell-annotation--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills single-cell-annotation --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/legacy/single-cell-annotation .gemini/skills/single-cell-annotation && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "single-cell-annotation" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation into .gemini/skills/single-cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install jaechang-hits/SciAgent-Skills single-cell-annotationInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/legacy/single-cell-annotation .github/skills/single-cell-annotation && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "single-cell-annotation" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation into .github/skills/single-cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install jaechang-hits/SciAgent-Skills single-cell-annotation --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/jaechang-hits/SciAgent-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/legacy/single-cell-annotation .opencode/skills/single-cell-annotation && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "single-cell-annotation" agent skill from https://github.com/jaechang-hits/SciAgent-Skills/tree/main/legacy/single-cell-annotation into .opencode/skills/single-cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "single-cell-annotation", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
single-cell-annotation- GitHub stars
- 371
- Used in
- 2 other repos
- Token cost
- ~3.2k tokens
- SKILL.md length
- 1,237 words
- Files
- 1
- Skills in repo
- 169
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
- Works in 7 steps: Manual Marker-Based Annotation → Automated Annotation → Reference-Based Label Transfer → …
- Tasks that involve Bioinformatics
- SKILL.md covers Metadata, Overview, Key Concepts and Decision Framework, plus 8 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Single Cell Annotation is an agent skill from jaechang-hits/SciAgent-Skills. Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
Its SKILL.md is about 3.2k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: 197 bioinformatics & life science skills for Claude Code and AI agents — BixBench 92.0% accuracy. RNA-seq, single-cell, drug discovery, proteomics, and more. Powers OmicsHorizon.
When your agent uses it
- Tasks that involve Bioinformatics
Example prompts
- “/single-cell-annotation”
Requirements
- Python 3
Workflow steps
7 steps, taken from the step headings in SKILL.md.
- Manual Marker-Based Annotation
- Automated Annotation
- Reference-Based Label Transfer
- Quality Control First
- Initial Marker-Based Assessment
- Use Automated Tools for Validation
- Reference-Based Refinement
What it can do on your machine
Read from SKILL.md and the folder at commit 82c862c. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
No scripts in the folder and no shell commands in SKILL.md (its code samples are python).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
sc-best-practices.orgscanpy.readthedocs.iocelltypist.orgscarches.readthedocs.iosatijalab.orgpanglaodb.sebio-bigdata.hrbmu.edu.cnhumancellatlas.org
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Single Cell Annotation loads about 3.2k tokens when it runs. Until then it costs about 41 tokens; SKILL.md has 1,237 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 1,237 words (~3,161 tokens).
“Short Description: Best practices for annotating cell types in single-cell RNA-seq data using marker-based, automated, and reference-based approaches.”
- name
- single-cell-annotation
- license
- open
Files
Just SKILL.md in legacy/single-cell-annotation of jaechang-hits/SciAgent-Skills.
Open the folder on GitHubat commit 82c862c
Used in 2 other repositories
We found 2 copies of this SKILL.md (exact, near-identical or edited) in other folders, from 2 other GitHub owners. This page covers the copy in jaechang-hits/SciAgent-Skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Single Cell Annotation next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Single Cell Annotation this skilljaechang-hits/SciAgent-Skills | 371 | 2 repos | ~3.2k | Automated safety check: Pass | Custom licence | |
| Alphagenome Single Variant Analysisgoogle-deepmind/science-skills | 3.2k | 2 repos | ~3k | Automated safety check: Notes | Apache-2.0 | |
| 13C Metabolic Flux AnalysisK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.2k | Automated safety check: Pass | MIT | |
| Clinvar Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.9k | Automated safety check: Notes | Apache-2.0 | |
| Metabolic Study Planneraiming-lab/AutoResearchClaw | 15k | — | ~1.9k | Automated safety check: Pass | MIT | |
| Dbsnp Databasegoogle-deepmind/science-skills | 3.2k | 2 repos | ~3.4k | Automated safety check: Notes | Apache-2.0 |
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Related
Categories
Questions about Single Cell Annotation
What does Single Cell Annotation do?
Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches. Single Cell Annotation is an agent skill from jaechang-hits/SciAgent-Skills. Best practices for single-cell RNA-seq cell type annotation including marker-based, reference-based, and automated classification approaches.
When should I use Single Cell Annotation?
Single Cell Annotation fits situations like: tasks that involve Bioinformatics.
How do I install Single Cell Annotation in Claude Code?
Run `npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation -a claude-code`. Or copy the skill folder (legacy/single-cell-annotation in jaechang-hits/SciAgent-Skills) into .claude/skills/single-cell-annotation in your project. Claude Code loads it when a task matches its description.
How do I install Single Cell Annotation in Codex?
Run `npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation -a codex`. Or copy the skill folder (legacy/single-cell-annotation in jaechang-hits/SciAgent-Skills) into .agents/skills/single-cell-annotation in your project. Codex loads it when a task matches its description.
Can I use Single Cell Annotation in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add jaechang-hits/SciAgent-Skills --skill single-cell-annotation -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/single-cell-annotation, .gemini/skills/single-cell-annotation, .github/skills/single-cell-annotation and .opencode/skills/single-cell-annotation in your project.
What does Single Cell Annotation need to run?
SKILL.md names no scripts, command-line tools or credentials: Single Cell Annotation is instructions for the agent only. Our summary lists: Python 3.
Does Single Cell Annotation access the network?
SKILL.md names 8 domains. As links in the text: sc-best-practices.org, scanpy.readthedocs.io, celltypist.org, scarches.readthedocs.io, satijalab.org, panglaodb.se, bio-bigdata.hrbmu.edu.cn and humancellatlas.org. This is read from the text; nothing was executed.
Is Single Cell Annotation safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Single Cell Annotation use?
Single Cell Annotation has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Single Cell Annotation use?
About 3.2k tokens (SKILL.md is roughly 13k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Single Cell Annotation?
Skills that share tags, products or a category with Single Cell Annotation: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Clinvar Database (google-deepmind/science-skills, 3.2k stars) and Metabolic Study Planner (aiming-lab/AutoResearchClaw, 15k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Single Cell Annotation?
jaechang-hits (a GitHub user) maintains it in jaechang-hits/SciAgent-Skills, which has 371 GitHub stars. The repository holds 169 skills in this directory. The repository was last updated on September 29, 2026.
Source: jaechang-hits/SciAgent-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.