Scanpy Single-Cell Analysis
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.
Install Cell Annotation
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill cell-annotation -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills 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/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bioclaw/cell-annotation .claude/skills/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 "cell-annotation" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw/cell-annotation into .claude/skills/cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw/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 BioTender-max/awesome-bio-agent-skills --skill cell-annotation -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills cell-annotation --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bioclaw/cell-annotation .agents/skills/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 "cell-annotation" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw/cell-annotation into .agents/skills/cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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 BioTender-max/awesome-bio-agent-skills --skill cell-annotation -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills cell-annotation --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bioclaw/cell-annotation .cursor/skills/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 "cell-annotation" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw/cell-annotation into .cursor/skills/cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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/BioTender-max/awesome-bio-agent-skills.git --path skills/bioclaw/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 BioTender-max/awesome-bio-agent-skills --skill cell-annotation -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills cell-annotation --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bioclaw/cell-annotation .gemini/skills/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 "cell-annotation" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw/cell-annotation into .gemini/skills/cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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 BioTender-max/awesome-bio-agent-skills 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 BioTender-max/awesome-bio-agent-skills --skill cell-annotation -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bioclaw/cell-annotation .github/skills/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 "cell-annotation" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw/cell-annotation into .github/skills/cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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 BioTender-max/awesome-bio-agent-skills --skill 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 BioTender-max/awesome-bio-agent-skills cell-annotation --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/BioTender-max/awesome-bio-agent-skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bioclaw/cell-annotation .opencode/skills/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 "cell-annotation" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw/cell-annotation into .opencode/skills/cell-annotation/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "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
cell-annotation- GitHub stars
- 197
- Used in
- 1 other repo
- Token cost
- ~1.2k tokens
- SKILL.md length
- 469 words
- Files
- 3
- Skills in repo
- 18
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.
- Works in 5 steps: Inspect markers before automation → Choose the annotation level → Run reference-based annotation → …
- Tasks that involve Bioinformatics
- SKILL.md covers Version Compatibility, Overview, When To Use This Skill and Quick Route, plus 12 more sections
- Calls python
What it does
Cell Annotation is an agent skill from BioTender-max/awesome-bio-agent-skills. Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.
Its SKILL.md is about 1.2k tokens, which your agent loads only when the skill is triggered. The skill folder holds 2 other files (for example `commands_and_thresholds.md` and `technical_reference.md`).
It sits in Research & Science, covering Bioinformatics. It works with Scanpy. The repository describes itself as: A curated collection of AI agent skills for biomedical research, covering genomics, proteomics, single-cell analysis, clinical AI, and protein design.
When your agent uses it
- Tasks that involve Bioinformatics
Example prompts
- “/cell-annotation”
Requirements
- Python 3
Workflow steps
5 steps, taken from the step headings in SKILL.md.
- Inspect markers before automation
- Choose the annotation level
- Run reference-based annotation
- Curate with markers and cluster context
- Export both raw and final labels
What it can do on your machine
Read from SKILL.md and the folder at commit 8cbdd18. 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
Shell commands in SKILL.md call:
python
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md.
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
Cell Annotation loads about 1.2k tokens when it runs. Until then it costs about 42 tokens; SKILL.md has 469 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 469 words (~1,154 tokens).
- name
- cell-annotation
- tool_type
- python
- primary_tool
- CellTypist
Files
SKILL.md and 2 other files in skills/bioclaw/cell-annotation of BioTender-max/awesome-bio-agent-skills.
- SKILL.md
- commands_and_thresholds.md
- technical_reference.md
Open the folder on GitHubat commit 8cbdd18
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in BioTender-max/awesome-bio-agent-skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
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 |
|---|---|---|---|---|---|---|
| Cell Annotation this skillBioTender-max/awesome-bio-agent-skills | 197 | 1 repos | ~1.2k | Automated safety check: Pass | Custom licence | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 32k | 16 repos | ~2.8k | Automated safety check: Pass | MIT | |
| Single Cell Rna AnalysisPKU-YuanGroup/OpenAI4S | 617 | — | ~1.3k | Automated safety check: Pass | MIT | |
| Anndatadavila7/claude-code-templates | 32k | 12 repos | ~2.5k | Automated safety check: Pass | MIT | |
| Cellxgene Censusdavila7/claude-code-templates | 32k | 11 repos | ~3.8k | Automated safety check: Pass | MIT | |
| Sc MarkersTianGzlab/OmicsClaw | 161 | 1 repos | ~2.2k | Automated safety check: Pass | Apache-2.0 |
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Single Cell Rna Analysis
PKU-YuanGroup/OpenAI4S
Reproducible Scanpy workflow for human or mouse 10x scRNA-seq and snRNA-seq count matrices: single-sample descriptive QC, clustering and annotation, or comparative donor-aware pseudobulk DE and Milo…
Anndata
davila7/claude-code-templates
This skill should be used when working with annotated data matrices in Python, particularly for single-cell genomics analysis, managing experimental measurements with metadata, or handling…
Cellxgene Census
davila7/claude-code-templates
Query CZ CELLxGENE Census (61M+ cells). An agent skill from davila7/claude-code-templates.
Sc Markers
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Load when ranking cluster-level marker genes from a clustered single-cell AnnData via Scanpy Wilcoxon / t-test / logreg or COSG specificity.
Bulk Rnaseq
K-Dense-AI/scientific-agent-skills
Prepares bulk RNA-seq FASTQ, Salmon, STAR or featureCounts output for gene-level differential expression.
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Related
Works with
Categories
Questions about Cell Annotation
What does Cell Annotation do?
Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation. Cell Annotation is an agent skill from BioTender-max/awesome-bio-agent-skills. Automated and marker-guided single-cell cell type annotation using CellTypist, marker review, reference transfer, and confidence-aware label curation.
When should I use Cell Annotation?
Cell Annotation fits situations like: tasks that involve Bioinformatics.
How do I install Cell Annotation in Claude Code?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill cell-annotation -a claude-code`. Or copy the skill folder (skills/bioclaw/cell-annotation in BioTender-max/awesome-bio-agent-skills) into .claude/skills/cell-annotation in your project. Claude Code loads it when a task matches its description.
How do I install Cell Annotation in Codex?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill cell-annotation -a codex`. Or copy the skill folder (skills/bioclaw/cell-annotation in BioTender-max/awesome-bio-agent-skills) into .agents/skills/cell-annotation in your project. Codex loads it when a task matches its description.
Can I use 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 BioTender-max/awesome-bio-agent-skills --skill 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/cell-annotation, .gemini/skills/cell-annotation, .github/skills/cell-annotation and .opencode/skills/cell-annotation in your project.
What does Cell Annotation need to run?
Going by SKILL.md and its folder, Cell Annotation needs the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Cell Annotation access the network?
SKILL.md contains no URLs. Any network use would come from the scripts or tools the agent runs. This is read from the text; nothing was executed.
Is 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 Cell Annotation use?
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 Cell Annotation use?
About 1.2k tokens (SKILL.md is roughly 4.6k 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 Cell Annotation?
Skills that share tags, products or a category with Cell Annotation: Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars), Single Cell Rna Analysis (PKU-YuanGroup/OpenAI4S, 617 stars), Anndata (davila7/claude-code-templates, 32k stars) and Cellxgene Census (davila7/claude-code-templates, 32k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Cell Annotation?
BioTender-max (a GitHub user) maintains it in BioTender-max/awesome-bio-agent-skills, which has 197 GitHub stars. The repository holds 18 skills in this directory. The repository was last updated on July 1, 2026.
Source: BioTender-max/awesome-bio-agent-skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.