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.
Candidate gene evidence from perturbation, dependency, resistance, sensitivity, viability, or assay-context records.
Install Functional Genomics
$ npx skills add exon-research/genomi --skill functional-genomics -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install exon-research/genomi functional-genomics --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/exon-research/genomi.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/functional-genomics .claude/skills/functional-genomics && 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 "functional-genomics" agent skill from https://github.com/exon-research/genomi/tree/master/skills/functional-genomics into .claude/skills/functional-genomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "functional-genomics", 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/exon-research/genomi/tree/master/skills/functional-genomicsType 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 exon-research/genomi --skill functional-genomics -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install exon-research/genomi functional-genomics --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/functional-genomics .agents/skills/functional-genomics && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "functional-genomics" agent skill from https://github.com/exon-research/genomi/tree/master/skills/functional-genomics into .agents/skills/functional-genomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "functional-genomics", 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 exon-research/genomi --skill functional-genomics -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install exon-research/genomi functional-genomics --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/functional-genomics .cursor/skills/functional-genomics && 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 "functional-genomics" agent skill from https://github.com/exon-research/genomi/tree/master/skills/functional-genomics into .cursor/skills/functional-genomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "functional-genomics", 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/exon-research/genomi.git --path skills/functional-genomics--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 exon-research/genomi --skill functional-genomics -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install exon-research/genomi functional-genomics --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/functional-genomics .gemini/skills/functional-genomics && 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 "functional-genomics" agent skill from https://github.com/exon-research/genomi/tree/master/skills/functional-genomics into .gemini/skills/functional-genomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "functional-genomics", 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 exon-research/genomi functional-genomicsInstalls 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 exon-research/genomi --skill functional-genomics -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/functional-genomics .github/skills/functional-genomics && 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 "functional-genomics" agent skill from https://github.com/exon-research/genomi/tree/master/skills/functional-genomics into .github/skills/functional-genomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "functional-genomics", 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 exon-research/genomi --skill functional-genomics -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install exon-research/genomi functional-genomics --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/exon-research/genomi.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/functional-genomics .opencode/skills/functional-genomics && 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 "functional-genomics" agent skill from https://github.com/exon-research/genomi/tree/master/skills/functional-genomics into .opencode/skills/functional-genomics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "functional-genomics", 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
functional-genomics- GitHub stars
- 484
- Token cost
- ~2k tokens
- SKILL.md length
- 929 words
- Files
- 1
- Skills in repo
- 20
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Candidate gene evidence from perturbation, dependency, resistance, sensitivity, viability, or assay-context records.
- Works in 7 steps: Extract candidate gene symbols and the… → Call… → Call… → …
- Tasks that involve Bioinformatics
- SKILL.md covers Contract, Tool Flow, Source Record Shape and Cross-Capability Synthesis, plus 1 more section
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Functional Genomics is an agent skill from exon-research/genomi. Candidate gene evidence from perturbation, dependency, resistance, sensitivity, viability, or assay-context records.
Its SKILL.md is about 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: Local-first, open-source Claude Science alternative, before Claude Science is a thing. Turn your AI agent into personal DNA expert. The licence is Apache-2.0.
When your agent uses it
- Tasks that involve Bioinformatics
Example prompts
- “/functional-genomics”
Workflow steps
7 steps, taken from the first numbered list in SKILL.md.
- Extract candidate gene symbols and the requested context: organism, cell
- Call functional_genomics.compare_gene_perturbation for the normal flow. It
- Call functional_genomics.retrieve_perturbation_records only for explicit
- Call functional_genomics.query_geo when the advantage is public source
- If the source is a local CSV/TSV result table, call
- Pass supplied, imported, or retrieved source records to
- Use verified perturbation-source evidence when the user asks for only the gene
What it can do on your machine
Read from SKILL.md and the folder at commit 1df4f5b. 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.
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
Functional Genomics loads about 2k tokens when it runs. Until then it costs about 34 tokens; SKILL.md has 929 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
The full file from exon-research/genomi at commit 1df4f5b, republished under its Apache-2.0 licence (© exon-research). 929 words, ~2,010 tokens.
Download SKILL.mdSave it as
.claude/skills/functional-genomics/SKILL.md (or your agent's skills folder).- name
- functional-genomics
- description
- Candidate gene evidence from perturbation, dependency, resistance, sensitivity, viability, or assay-context records.
- tools
- functional_genomics.retrieve_perturbation_records, functional_genomics.query_geo, functional_genomics.import_perturbation_table…
- mutating
- true
Functional Genomics Perturbation Evidence
Retrieve functional-genomics perturbation evidence for a declared experimental context plus candidate genes. Screens are one supported perturbation experiment subtype, not the capability name.
Contract
Perturbation evidence comes from native public retrieval, user-provided local tables, reviewed stored research, or explicitly supplied source records. Generic gene biology can explain a result, but it should not outrank direct perturbation-source evidence.
Direct support is source-verified perturbation evidence. Source records carry verified fields or support spans for the requested cell line, perturbation, assay/readout, and candidate gene relationship; broader biology remains adjacent or plausibility-only evidence.
Native coverage currently includes BioGRID ORCS when a BioGRID ORCS access key is available, DepMap CRISPR gene-effect release tables when a CSV URL or path is configured, and bounded NCBI GEO metadata/table discovery. GEO's advantage is source discovery for public or published perturbation datasets: SeriesMatrix files, supplementary tables, and accession-indexed study records that curated screen APIs may not expose for the requested cell line, perturbation, assay, or readout. If native sources cannot be queried, the response makes that coverage state visible rather than weak ranking evidence.
Tool Flow
- Extract candidate gene symbols and the requested context: organism, cell line, perturbation, assay, phenotype, resistance, sensitivity, viability, or readout.
- Call
functional_genomics.compare_gene_perturbationfor the normal flow. It retrieves native public perturbation records when configured, verifies source records, and returns candidate evidence rows. - Call
functional_genomics.retrieve_perturbation_recordsonly for explicit native-source inspection, coverage debugging, or source availability review. - Call
functional_genomics.query_geowhen the advantage is public source discovery: the question mentions a published/public screen dataset, study accession, supplementary table, SeriesMatrix-style file, or compare has insufficient BioGRID/DepMap/stored evidence for a requested perturbation context that likely came from a public study. The user does not need to name GEO. GEO metadata alone is not direct evidence; direct support still requires table-derived, source-verified candidate gene and perturbation-context fields. - If the source is a local CSV/TSV result table, call
functional_genomics.import_perturbation_tablefirst. - Pass supplied, imported, or retrieved source records to
functional_genomics.compare_gene_perturbation; it verifies source records before comparing candidate genes. - Use verified perturbation-source evidence when the user asks for only the gene
symbol. Audit
decision_evidencebefore explaining the result.
functional_genomics.compare_gene_perturbation returns evidence rather than a universal
answer. If source records do not support an identifier-only answer, do not invent
a gene; state the source gap or gather better source records.
Source Record Shape
functional_genomics.compare_gene_perturbation accepts reviewed source records. Prefer records that
include the source title or URL, named genes, the source-backed finding, source
type, and any verified perturbation context such as cell line, perturbation, assay,
phenotype, readout, PMID, or DOI.
When a paper or dataset directly supports the requested perturbation context, include the specific source-backed spans that verify the cell line, perturbation, assay/readout, and gene relationship. Generic pathway or co-mention literature should remain adjacent evidence.
Direct perturbation-source context outranks generic literature or pathway plausibility only when source-backed fields verify the context. If no source records are supplied, or if records are generic literature without context verification, the tool cannot fairly make a high-support ranking.
Cross-Capability Synthesis
A scope-limited result from this capability is not a final user-facing answer when other Genomi capabilities can contribute orthogonal evidence to the same question. Returning "cannot answer" while applicable capabilities remain unexamined is a host-agent failure mode.
Tools
Show full SKILL.md (388 more words)Show less
functional_genomics.compare_gene_perturbation
Compare candidate genes by verified functional-genomics perturbation experiment evidence.
Use when: Retrieves native public perturbation experiment records when configured, verifies source records, and returns candidate-gene evidence rows for the declared perturbation context.
Why necessary: Screen and dependency questions need verified perturbation evidence, not inherited-variant or disease association evidence.
Example prompts: Which candidate gene is best supported by this CRISPR resistance screen?
Result semantics: Runs source-record verification before candidate comparison; generic literature stays separate from direct perturbation experiment evidence.
functional_genomics.import_perturbation_table
Extract verified perturbation experiment source records from a local CSV or TSV result table.
Use when: The agent has a local CSV/TSV perturbation, dependency, viability, resistance, or supplementary result table and needs source records before candidate comparison.
Why necessary: User-supplied screen tables need structured extraction before they can support gene comparisons.
Result semantics: Extracts table rows into source records and verifies row-level genes plus perturbation context; it does not select the answer gene.
functional_genomics.query_geo
Query NCBI GEO metadata and bounded public study tables for functional-genomics perturbation source records.
Use when: The advantage is public dataset discovery: a published/public screen, study accession, supplementary table, SeriesMatrix-style file, or an under-covered perturbation context where curated sources did not provide direct source records.
Why necessary: GEO can find source-backed tables for study-specific cell lines, perturbations, assays, and readouts that BioGRID ORCS, DepMap, or stored reviewed records may not cover; it keeps metadata-only hits separate from direct perturbation evidence.
Result semantics: Returns GEO metadata hits, download candidates with skip reasons, and verified source records when candidate genes are supplied. Metadata-only matches never count as direct evidence; direct support requires source-verified gene plus requested perturbation context fields.
functional_genomics.retrieve_perturbation_records
Retrieve native public functional-genomics perturbation records from BioGRID ORCS and DepMap for candidate genes and declared experimental context.
Use when: Explicit native-source inspection, source availability review, or coverage debugging for BioGRID ORCS and configured DepMap perturbation records.
Why necessary: Raw native-source retrieval lets agents inspect what BioGRID ORCS or DepMap returned, or why a native source was unavailable, without running candidate comparison.
Result semantics: Returns native functional-genomics source records from BioGRID ORCS and configured DepMap release tables; it does not select the final gene. For normal candidate-gene comparison, use functional_genomics.compare_gene_perturbation directly because it can retrieve native records when configured. BioGRID ORCS requires an access key; DepMap requires a configured public CRISPR gene-effect CSV URL or path.
© exon-research, Apache-2.0. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file
Files
Just SKILL.md in skills/functional-genomics of exon-research/genomi.
Open the folder on GitHubat commit 1df4f5b
Compare with similar skills
Functional Genomics 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 |
|---|---|---|---|---|---|---|
| Functional Genomics this skillexon-research/genomi | 484 | — | ~2k | Automated safety check: Pass | Apache-2.0 | |
| 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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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.
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Related
Categories
Questions about Functional Genomics
What does Functional Genomics do?
Candidate gene evidence from perturbation, dependency, resistance, sensitivity, viability, or assay-context records. Functional Genomics is an agent skill from exon-research/genomi. Candidate gene evidence from perturbation, dependency, resistance, sensitivity, viability, or assay-context records.
When should I use Functional Genomics?
Functional Genomics fits situations like: tasks that involve Bioinformatics.
How do I install Functional Genomics in Claude Code?
Run `npx skills add exon-research/genomi --skill functional-genomics -a claude-code`. Or copy the skill folder (skills/functional-genomics in exon-research/genomi) into .claude/skills/functional-genomics in your project. Claude Code loads it when a task matches its description.
How do I install Functional Genomics in Codex?
Run `npx skills add exon-research/genomi --skill functional-genomics -a codex`. Or copy the skill folder (skills/functional-genomics in exon-research/genomi) into .agents/skills/functional-genomics in your project. Codex loads it when a task matches its description.
Can I use Functional Genomics 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 exon-research/genomi --skill functional-genomics -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/functional-genomics, .gemini/skills/functional-genomics, .github/skills/functional-genomics and .opencode/skills/functional-genomics in your project.
What does Functional Genomics need to run?
SKILL.md names no scripts, command-line tools or credentials: Functional Genomics is instructions for the agent only.
Does Functional Genomics 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 Functional Genomics 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 Functional Genomics use?
Functional Genomics is published under the Apache-2.0 licence (the repository's licence). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Functional Genomics use?
About 2k tokens (SKILL.md is roughly 8k 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 Functional Genomics?
Skills that share tags, products or a category with Functional Genomics: 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 Functional Genomics?
exon-research (a GitHub organization) maintains it in exon-research/genomi, which has 484 GitHub stars. The repository holds 20 skills in this directory. The repository was last updated on August 31, 2026.
Source: exon-research/genomi on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.