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.
Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R.
Install Biogeobears
$ npx skills add aiskillstore/marketplace --skill biogeobears -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install aiskillstore/marketplace biogeobears --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/aiskillstore/marketplace.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/brunoasm/biogeobears .claude/skills/biogeobears && 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 "biogeobears" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/brunoasm/biogeobears into .claude/skills/biogeobears/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biogeobears", 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/aiskillstore/marketplace/tree/main/skills/brunoasm/biogeobearsType 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 aiskillstore/marketplace --skill biogeobears -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install aiskillstore/marketplace biogeobears --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/brunoasm/biogeobears .agents/skills/biogeobears && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "biogeobears" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/brunoasm/biogeobears into .agents/skills/biogeobears/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biogeobears", 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 aiskillstore/marketplace --skill biogeobears -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install aiskillstore/marketplace biogeobears --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/brunoasm/biogeobears .cursor/skills/biogeobears && 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 "biogeobears" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/brunoasm/biogeobears into .cursor/skills/biogeobears/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biogeobears", 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/aiskillstore/marketplace.git --path skills/brunoasm/biogeobears--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 aiskillstore/marketplace --skill biogeobears -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install aiskillstore/marketplace biogeobears --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/brunoasm/biogeobears .gemini/skills/biogeobears && 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 "biogeobears" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/brunoasm/biogeobears into .gemini/skills/biogeobears/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biogeobears", 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 aiskillstore/marketplace biogeobearsInstalls 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 aiskillstore/marketplace --skill biogeobears -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/brunoasm/biogeobears .github/skills/biogeobears && 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 "biogeobears" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/brunoasm/biogeobears into .github/skills/biogeobears/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biogeobears", 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 aiskillstore/marketplace --skill biogeobears -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install aiskillstore/marketplace biogeobears --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/aiskillstore/marketplace.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/brunoasm/biogeobears .opencode/skills/biogeobears && 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 "biogeobears" agent skill from https://github.com/aiskillstore/marketplace/tree/main/skills/brunoasm/biogeobears into .opencode/skills/biogeobears/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "biogeobears", 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
biogeobears- GitHub stars
- 430
- Token cost
- ~4.5k tokens
- SKILL.md length
- 1,291 words
- Files
- 6 (incl. scripts, references)
- Skills in repo
- 1,044
- Repo updated
- First seen
- Licence
- None found
At a glance
Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R.
- Works in 5 steps: Gather Information → Validate and Prepare Input Files → Set Up Analysis Folder Structure → …
- Users request biogeographic reconstruction
- SKILL.md covers Overview, When to Use This Skill, Required Inputs and Workflow, plus 10 more sections
- Runs Python scripts from its folder; calls python, bash and claude
What it does
Biogeobears is an agent skill from aiskillstore/marketplace. Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R. Use when users request biogeographic reconstruction, ancestral range estimation, or want to analyze species distributions on phylogenies. Handles input file validation, data reformatting, RMarkdown workflow generation, and result visualization.
Its SKILL.md is about 4.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 7 other files, including scripts and reference files (for example `README.md`, `references/biogeobears_details.md` and `scripts/validate_geography_file.py`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Security-audited skills for Claude, Codex & Claude Code. One-click install, quality verified.
When your agent uses it
- Users request biogeographic reconstruction
- Ancestral range estimation
- Want to analyze species distributions on phylogenies
Example prompts
- “/biogeobears”
Requirements
- Python 3
Workflow steps
5 steps, taken from the step headings in SKILL.md.
- Gather Information
- Validate and Prepare Input Files
- Set Up Analysis Folder Structure
- Generate RMarkdown Analysis Script
- Create README Documentation
What it can do on your machine
Read from SKILL.md and the folder at commit 755bc35. 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
Ships 2 files in scripts/ (Python), which the agent can run.
Shell commands in SKILL.md call:
pythonbashclaude
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):
phylo.wikidot.com
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
Biogeobears loads about 4.5k tokens when it runs, and up to ~6.9k if it reads all its reference files. Until then it costs about 84 tokens; SKILL.md has 1,291 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); the scripts in this folder are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 1,291 words (~4,503 tokens).
“BioGeoBEARS (BioGeography with Bayesian and Likelihood Evolutionary Analysis in R Scripts) performs probabilistic inference of ancestral geographic ranges on phylogenetic trees. This skill helps set up complete biogeographic analyses by:”
- name
- biogeobears
Files
SKILL.md and 5 other files (scripts, references) in skills/brunoasm/biogeobears of aiskillstore/marketplace.
- SKILL.md
- README.md
- references/biogeobears_details.md
- scripts/biogeobears_analysis_template.Rmd
- scripts/validate_geography_file.py
- skill-report.json
Open the folder on GitHubat commit 755bc35
Compare with similar skills
Biogeobears 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 |
|---|---|---|---|---|---|---|
| Biogeobears this skillaiskillstore/marketplace | 430 | — | ~4.5k | Automated safety check: Pass | None | |
| 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 |
Similar skills
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Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
Clinvar Database
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A skill your agent uses when needing clinical significance, pathogenicity classifications (e.g., Pathogenic, Benign, VUS), clinical evidence rationales, or finding "hard positive" benchmark controls…
Metabolic Study Planner
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Turns a broad metabolic modelling topic into a concrete, paper-shaped plan with organism, model, perturbations, metrics and figures before any FBA code is written.
Dbsnp Database
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A skill your agent uses when you want to look up, map, and search for short genetic variants (SNPs, indels) in NCBI's dbSNP database.
MFA Pipeline Orchestrator
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Runs a metabolic flux analysis from model loading to phenotype prediction and figures by handing work to four sub-agents in sequence.
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Related
Categories
Questions about Biogeobears
What does Biogeobears do?
Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R. Biogeobears is an agent skill from aiskillstore/marketplace. Set up and execute phylogenetic biogeographic analyses using BioGeoBEARS in R.
When should I use Biogeobears?
Biogeobears fits situations like: users request biogeographic reconstruction; ancestral range estimation; want to analyze species distributions on phylogenies.
How do I install Biogeobears in Claude Code?
Run `npx skills add aiskillstore/marketplace --skill biogeobears -a claude-code`. Or copy the skill folder (skills/brunoasm/biogeobears in aiskillstore/marketplace) into .claude/skills/biogeobears in your project. Claude Code loads it when a task matches its description.
How do I install Biogeobears in Codex?
Run `npx skills add aiskillstore/marketplace --skill biogeobears -a codex`. Or copy the skill folder (skills/brunoasm/biogeobears in aiskillstore/marketplace) into .agents/skills/biogeobears in your project. Codex loads it when a task matches its description.
Can I use Biogeobears 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 aiskillstore/marketplace --skill biogeobears -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/biogeobears, .gemini/skills/biogeobears, .github/skills/biogeobears and .opencode/skills/biogeobears in your project.
What does Biogeobears need to run?
Going by SKILL.md and its folder, Biogeobears needs Python for the scripts in its folder and the command-line tools its instructions call (python, bash and claude). Our summary lists: Python 3.
Does Biogeobears access the network?
SKILL.md names 1 domain. As links in the text: phylo.wikidot.com. This is read from the text; nothing was executed.
Is Biogeobears 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. The check reads SKILL.md only: the scripts in the folder are not scanned, so read them before running anything.
What licence does Biogeobears use?
No licence was found for Biogeobears or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Biogeobears use?
About 4.5k tokens (SKILL.md is roughly 18k 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 2.4k tokens, read only when the agent opens those files.
What are the alternatives to Biogeobears?
Skills that share tags, products or a category with Biogeobears: 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 Biogeobears?
aiskillstore (a GitHub organization) maintains it in aiskillstore/marketplace, which has 430 GitHub stars. The repository holds 1,044 skills in this directory. The repository was last updated on October 9, 2026.
Source: aiskillstore/marketplace on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.