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.
Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list.
Install Bulkrna Enrichment
$ npx skills add TianGzlab/OmicsClaw --skill bulkrna-enrichment -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-enrichment --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/TianGzlab/OmicsClaw.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bulkrna/bulkrna-enrichment .claude/skills/bulkrna-enrichment && 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 "bulkrna-enrichment" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-enrichment into .claude/skills/bulkrna-enrichment/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-enrichment", 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/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-enrichmentType 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 TianGzlab/OmicsClaw --skill bulkrna-enrichment -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-enrichment --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bulkrna/bulkrna-enrichment .agents/skills/bulkrna-enrichment && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bulkrna-enrichment" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-enrichment into .agents/skills/bulkrna-enrichment/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-enrichment", 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 TianGzlab/OmicsClaw --skill bulkrna-enrichment -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-enrichment --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bulkrna/bulkrna-enrichment .cursor/skills/bulkrna-enrichment && 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 "bulkrna-enrichment" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-enrichment into .cursor/skills/bulkrna-enrichment/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-enrichment", 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/TianGzlab/OmicsClaw.git --path skills/bulkrna/bulkrna-enrichment--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 TianGzlab/OmicsClaw --skill bulkrna-enrichment -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-enrichment --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bulkrna/bulkrna-enrichment .gemini/skills/bulkrna-enrichment && 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 "bulkrna-enrichment" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-enrichment into .gemini/skills/bulkrna-enrichment/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-enrichment", 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 TianGzlab/OmicsClaw bulkrna-enrichmentInstalls 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 TianGzlab/OmicsClaw --skill bulkrna-enrichment -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bulkrna/bulkrna-enrichment .github/skills/bulkrna-enrichment && 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 "bulkrna-enrichment" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-enrichment into .github/skills/bulkrna-enrichment/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-enrichment", 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 TianGzlab/OmicsClaw --skill bulkrna-enrichment -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-enrichment --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/TianGzlab/OmicsClaw.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bulkrna/bulkrna-enrichment .opencode/skills/bulkrna-enrichment && 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 "bulkrna-enrichment" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-enrichment into .opencode/skills/bulkrna-enrichment/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-enrichment", 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
bulkrna-enrichment- GitHub stars
- 161
- Token cost
- ~860 tokens
- SKILL.md length
- 305 words
- Files
- 11 (incl. references)
- Skills in repo
- 88
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list.
- Tasks that involve Bioinformatics
- SKILL.md covers Purpose, Inputs & Outputs, API and Key CLI, plus 2 more sections
- Runs Python scripts from its folder; calls python
What it does
Bulkrna Enrichment is an agent skill from TianGzlab/OmicsClaw. Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list. Skip when the input is single-cell (use sc-enrichment); the input is spatial (use spatial-enrichment); metabolite pathways (use metabolomics-pathway-enrichment).
Its SKILL.md is about 860 tokens, which your agent loads only when the skill is triggered. The skill folder holds 13 other files, including reference files (for example `_api.py`, `bulkrna_enrichment.py` and `examples/example_step.py`).
It sits in Research & Science, covering Bioinformatics. The repository describes itself as: Conversational & memory-enabled AI research partner for multi-omics analysis. CLI + Desktop App (installers in Releases). From biological idea to full research paper. The licence is Apache-2.0.
When your agent uses it
- Tasks that involve Bioinformatics
Example prompts
- “/bulkrna-enrichment”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit 90a3bec. 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 script files (Python), which the agent can run.
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
Bulkrna Enrichment loads about 860 tokens when it runs, and up to ~1.5k if it reads all its reference files. Until then it costs about 65 tokens; SKILL.md has 305 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 TianGzlab/OmicsClaw at commit 90a3bec, republished under its Apache-2.0 licence (© TianGzlab). 305 words, ~860 tokens.
Download SKILL.mdSave it as
.claude/skills/bulkrna-enrichment/SKILL.md (or your agent's skills folder). This skill also uses 10 other files; get the full folder from GitHub.- name
- bulkrna-enrichment
- description
- Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list. Skip when the input is single-cell (use sc-enrichment); the input is spatial (use spatial-enrichment); metabolite pathways (use metabolomics-pathway-enrichment).
- trigger
- bulk enrichment, pathway analysis, GSEA, ORA, GO enrichment, KEGG, bulk pathway
- tags
- bulkrna, enrichment, GSEA, ORA, GO, KEGG, Reactome, pathway
Bulk pathway enrichment
Purpose
Test differential-expression results against explicit pathway gene sets. ORA uses the union of those sets as its background; GSEA ranks all input genes. Gene identifiers must use the same namespace. R adapters are not implemented.
Inputs & Outputs
CLI input is a CSV with gene, log2FoldChange, pvalue, padj; --gene-set-file is a JSON mapping from pathway names to gene lists. The library accepts the table and mapping directly. CLI writes tables/enrichment_results.csv, tables/enrichment_significant.csv, report/result files and method-dependent figures.
API
<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->enrich(de_results, *, gene_sets, method='ora', padj_cutoff=0.05, lfc_cutoff=1.0, random_state=42)
Test pathway enrichment without choosing a reference database.
:param de_results: DataFrame with gene, log2FoldChange, pvalue and padj. :param gene_sets: Nonempty mapping from pathway names to unique gene lists. :param method: CLI default ora; gsea runs GSEApy prerank. :param padj_cutoff: CLI significance threshold, default 0.05. :param lfc_cutoff: Strict absolute fold-change threshold, default 1.0. :param random_state: Local permutation seed, legacy default 42. :returns: Enrichment DataFrame with execution diagnostics in attrs. :raises ValueError: Missing reference, invalid values or unsupported method.
run_info(result, *, keep=True)
Read tested terms, pathway universe and requested/executed methods.
:param result: DataFrame returned by enrich. :param keep: Default True; False removes diagnostic attrs. :returns: Diagnostic dictionary; empty after removal.
enrichment_figure(result)
Plot pathway adjusted significance without saving it.
:param result: Enrichment DataFrame with term and padj columns. :returns: matplotlib Figure. :raises KeyError: Required columns are missing.
<!-- api:end -->Key CLI
python skills/bulkrna/bulkrna-enrichment/bulkrna_enrichment.py --demo --output /tmp/bulkrna-enrichment
python skills/bulkrna/bulkrna-enrichment/bulkrna_enrichment.py --input de.csv --gene-set-file pathways.json --output results/enrichment --method oraGotchas
run_info(result)['background_genes']is the pathway-union background, not all measured genes. Choose reference sets accordingly.run_info(result)['executed_method']andfallback_reasondisclose fallback calculations. The built-in GSEA fallback is a mean-rank permutation test, not GSEA; fallback emits a warning.tables/enrichment_results.csvmay be empty when no terms overlap. Demo pathways are available only with--demo; real input requires an explicit reference.run_info(result)['method_used']distinguishes GSEApy and built-in calculations. The legacyora_randgsea_rflags now reject an unimplemented backend rather than silently changing it.
Dependencies
numpy, pandas, scipy, matplotlib, gseapy
© TianGzlab, 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
SKILL.md and 10 other files (references) in skills/bulkrna/bulkrna-enrichment of TianGzlab/OmicsClaw.
- SKILL.md
- _api.py
- bulkrna_enrichment.py
- examples/example_step.py
- references/methodology.md
- references/output_contract.md
- references/parameters.md
- tests/__init__.py
- tests/biomnibench_da12_2.py
- tests/test_api.py
- tests/test_bulkrna_enrichment.py
Open the folder on GitHubat commit 90a3bec
Compare with similar skills
Bulkrna Enrichment 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 |
|---|---|---|---|---|---|---|
| Bulkrna Enrichment this skillTianGzlab/OmicsClaw | 161 | — | ~860 | 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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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.
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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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Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation.
Bulkrna Coexpression
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Bulkrna De
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Bulkrna Deconvolution
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Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference.
Bulkrna Geneid Mapping
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Related
Categories
Questions about Bulkrna Enrichment
What does Bulkrna Enrichment do?
Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list. Bulkrna Enrichment is an agent skill from TianGzlab/OmicsClaw. Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list.
When should I use Bulkrna Enrichment?
Bulkrna Enrichment fits situations like: tasks that involve Bioinformatics.
How do I install Bulkrna Enrichment in Claude Code?
Run `npx skills add TianGzlab/OmicsClaw --skill bulkrna-enrichment -a claude-code`. Or copy the skill folder (skills/bulkrna/bulkrna-enrichment in TianGzlab/OmicsClaw) into .claude/skills/bulkrna-enrichment in your project. Claude Code loads it when a task matches its description.
How do I install Bulkrna Enrichment in Codex?
Run `npx skills add TianGzlab/OmicsClaw --skill bulkrna-enrichment -a codex`. Or copy the skill folder (skills/bulkrna/bulkrna-enrichment in TianGzlab/OmicsClaw) into .agents/skills/bulkrna-enrichment in your project. Codex loads it when a task matches its description.
Can I use Bulkrna Enrichment 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 TianGzlab/OmicsClaw --skill bulkrna-enrichment -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bulkrna-enrichment, .gemini/skills/bulkrna-enrichment, .github/skills/bulkrna-enrichment and .opencode/skills/bulkrna-enrichment in your project.
What does Bulkrna Enrichment need to run?
Going by SKILL.md and its folder, Bulkrna Enrichment needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Bulkrna Enrichment 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 Bulkrna Enrichment 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 Bulkrna Enrichment use?
Bulkrna Enrichment 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 Bulkrna Enrichment use?
About 860 tokens (SKILL.md is roughly 3.4k 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 632 tokens, read only when the agent opens those files.
What are the alternatives to Bulkrna Enrichment?
Skills that share tags, products or a category with Bulkrna Enrichment: 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 Bulkrna Enrichment?
TianGzlab (a GitHub organization) maintains it in TianGzlab/OmicsClaw, which has 161 GitHub stars. The repository holds 88 skills in this directory. The repository was last updated on October 7, 2026.
Source: TianGzlab/OmicsClaw on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.