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.
Workflow for paired or integrated single-cell RNA and ATAC analysis with multimodal latent spaces and regulatory interpretation.
Install Multiome Scatac
$ npx skills add BioTender-max/awesome-bio-agent-skills --skill multiome-scatac -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills multiome-scatac --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_hub/multiome-scatac .claude/skills/multiome-scatac && 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 "multiome-scatac" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw_hub/multiome-scatac into .claude/skills/multiome-scatac/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiome-scatac", 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_hub/multiome-scatacType 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 multiome-scatac -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills multiome-scatac --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_hub/multiome-scatac .agents/skills/multiome-scatac && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "multiome-scatac" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw_hub/multiome-scatac into .agents/skills/multiome-scatac/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiome-scatac", 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 multiome-scatac -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills multiome-scatac --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_hub/multiome-scatac .cursor/skills/multiome-scatac && 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 "multiome-scatac" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw_hub/multiome-scatac into .cursor/skills/multiome-scatac/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiome-scatac", 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_hub/multiome-scatac--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 multiome-scatac -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install BioTender-max/awesome-bio-agent-skills multiome-scatac --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_hub/multiome-scatac .gemini/skills/multiome-scatac && 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 "multiome-scatac" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw_hub/multiome-scatac into .gemini/skills/multiome-scatac/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiome-scatac", 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 multiome-scatacInstalls 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 multiome-scatac -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_hub/multiome-scatac .github/skills/multiome-scatac && 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 "multiome-scatac" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw_hub/multiome-scatac into .github/skills/multiome-scatac/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiome-scatac", 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 multiome-scatac -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 multiome-scatac --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_hub/multiome-scatac .opencode/skills/multiome-scatac && 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 "multiome-scatac" agent skill from https://github.com/BioTender-max/awesome-bio-agent-skills/tree/main/skills/bioclaw_hub/multiome-scatac into .opencode/skills/multiome-scatac/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiome-scatac", 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
multiome-scatac- GitHub stars
- 199
- Used in
- 1 other repo
- Token cost
- ~1.1k tokens
- SKILL.md length
- 496 words
- Files
- 3 (incl. references)
- Skills in repo
- 23
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
Workflow for paired or integrated single-cell RNA and ATAC analysis with multimodal latent spaces and regulatory interpretation.
- Works in 5 steps: QC both modalities → Create harmonized features → Integrate modalities → …
- 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
Multiome Scatac is an agent skill from BioTender-max/awesome-bio-agent-skills. Workflow for paired or integrated single-cell RNA and ATAC analysis with multimodal latent spaces and regulatory interpretation.
Its SKILL.md is about 1.1k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files, including reference files (for example `README.md` and `references/technical_reference.md`).
It sits in Research & Science, covering Bioinformatics. It works with Python. 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
- “/multiome-scatac”
Requirements
- Python 3
Workflow steps
5 steps, taken from the step headings in SKILL.md.
- QC both modalities
- Create harmonized features
- Integrate modalities
- Interpret regulatory signals
- Export multimodal state summaries
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
Multiome Scatac loads about 1.1k tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 36 tokens; SKILL.md has 496 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 496 words (~1,096 tokens).
“Reference examples assume recent stable releases of the preferred tools, especially scanpy and the other tools listed below.”
- name
- multiome-scatac
- tool_type
- python
- primary_tool
- scanpy
Files
SKILL.md and 2 other files (references) in skills/bioclaw_hub/multiome-scatac of BioTender-max/awesome-bio-agent-skills.
- SKILL.md
- README.md
- references/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
Multiome Scatac 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 |
|---|---|---|---|---|---|---|
| Multiome Scatac this skillBioTender-max/awesome-bio-agent-skills | 199 | 1 repos | ~1.1k | 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 | |
| Singlecell Qcxuzhougeng/wisp-science | 1k | — | ~1.6k | Automated safety check: Pass | AGPL-3.0 | |
| Trackplotygidtu/trackplot | 109 | — | ~1.9k | Automated safety check: Pass | BSD-3-Clause | |
| UniProt Database Accessdavila7/claude-code-templates | 32k | 14 repos | ~1.7k | Automated safety check: Pass | MIT |
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K-Dense-AI/scientific-agent-skills
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Singlecell Qc
xuzhougeng/wisp-science
A skill your agent uses when designing, reviewing, or implementing single-cell RNA-seq QC in Python or R with a human-in-the-loop, data-driven approach.
Trackplot
ygidtu/trackplot
Generate sashimi-style genome visualization plots (coverage, line, heatmap, IGV read-by-read, HiC, circRNA, motif) from BAM/bigWig/depth/HiC inputs.
UniProt Database Access
davila7/claude-code-templates
Queries the UniProt REST API directly to search proteins, fetch FASTA sequences, map IDs between databases and read Swiss-Prot and TrEMBL entries.
Spatial Transcriptomics
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End-to-end 10x Visium spatial transcriptomics analysis workflow with staged execution and human review gates.
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Related
Works with
Categories
Questions about Multiome Scatac
What does Multiome Scatac do?
Workflow for paired or integrated single-cell RNA and ATAC analysis with multimodal latent spaces and regulatory interpretation. Multiome Scatac is an agent skill from BioTender-max/awesome-bio-agent-skills. Workflow for paired or integrated single-cell RNA and ATAC analysis with multimodal latent spaces and regulatory interpretation.
When should I use Multiome Scatac?
Multiome Scatac fits situations like: tasks that involve Bioinformatics.
How do I install Multiome Scatac in Claude Code?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill multiome-scatac -a claude-code`. Or copy the skill folder (skills/bioclaw_hub/multiome-scatac in BioTender-max/awesome-bio-agent-skills) into .claude/skills/multiome-scatac in your project. Claude Code loads it when a task matches its description.
How do I install Multiome Scatac in Codex?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill multiome-scatac -a codex`. Or copy the skill folder (skills/bioclaw_hub/multiome-scatac in BioTender-max/awesome-bio-agent-skills) into .agents/skills/multiome-scatac in your project. Codex loads it when a task matches its description.
Can I use Multiome Scatac 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 multiome-scatac -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/multiome-scatac, .gemini/skills/multiome-scatac, .github/skills/multiome-scatac and .opencode/skills/multiome-scatac in your project.
What does Multiome Scatac need to run?
Going by SKILL.md and its folder, Multiome Scatac needs the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Multiome Scatac 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 Multiome Scatac 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 Multiome Scatac use?
Multiome Scatac 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 Multiome Scatac use?
About 1.1k tokens (SKILL.md is roughly 4.4k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full. Its references folder adds about 537 tokens, read only when the agent opens those files.
What are the alternatives to Multiome Scatac?
Skills that share tags, products or a category with Multiome Scatac: Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars), Singlecell Qc (xuzhougeng/wisp-science, 1k stars) and Trackplot (ygidtu/trackplot, 109 stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Multiome Scatac?
BioTender-max (a GitHub user) maintains it in BioTender-max/awesome-bio-agent-skills, which has 199 GitHub stars. The repository holds 23 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.