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 comparing gene expression between two conditions in bulk RNA-seq count data.
Install Bulkrna De
$ npx skills add TianGzlab/OmicsClaw --skill bulkrna-de -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-de --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-de .claude/skills/bulkrna-de && 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-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-de into .claude/skills/bulkrna-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-de", 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-deType 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-de -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-de --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-de .agents/skills/bulkrna-de && 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-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-de into .agents/skills/bulkrna-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-de", 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-de -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-de --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-de .cursor/skills/bulkrna-de && 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-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-de into .cursor/skills/bulkrna-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-de", 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-de--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-de -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install TianGzlab/OmicsClaw bulkrna-de --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-de .gemini/skills/bulkrna-de && 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-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-de into .gemini/skills/bulkrna-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-de", 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-deInstalls 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-de -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-de .github/skills/bulkrna-de && 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-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-de into .github/skills/bulkrna-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-de", 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-de -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-de --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-de .opencode/skills/bulkrna-de && 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-de" agent skill from https://github.com/TianGzlab/OmicsClaw/tree/main/skills/bulkrna/bulkrna-de into .opencode/skills/bulkrna-de/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bulkrna-de", 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-de- GitHub stars
- 161
- Token cost
- ~867 tokens
- SKILL.md length
- 326 words
- Files
- 10 (incl. references)
- Skills in repo
- 88
- Repo updated
- First seen
- Licence
- Apache-2.0
At a glance
Load when comparing gene expression between two conditions in bulk RNA-seq count data.
- 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 De is an agent skill from TianGzlab/OmicsClaw. Load when comparing gene expression between two conditions in bulk RNA-seq count data. Skip when the data is single-cell (use sc-de); spatial (use spatial-de); you need exon-level alternative splicing (use bulkrna-splicing).
Its SKILL.md is about 870 tokens, which your agent loads only when the skill is triggered. The skill folder holds 12 other files, including reference files (for example `_api.py`, `bulkrna_de.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-de”
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 De loads about 867 tokens when it runs, and up to ~1.6k if it reads all its reference files. Until then it costs about 59 tokens; SKILL.md has 326 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). 326 words, ~867 tokens.
Download SKILL.mdSave it as
.claude/skills/bulkrna-de/SKILL.md (or your agent's skills folder). This skill also uses 9 other files; get the full folder from GitHub.- name
- bulkrna-de
- description
- Load when comparing gene expression between two conditions in bulk RNA-seq count data. Skip when the data is single-cell (use sc-de); spatial (use spatial-de); you need exon-level alternative splicing (use bulkrna-splicing).
- trigger
- differential expression, DE analysis, DESeq2, volcano plot, fold change, DEGs, bulk DE
- tags
- bulkrna, differential-expression, DESeq2, volcano, MA-plot, fold-change
Bulk differential expression
Purpose
Compare two prefix-selected groups in a raw count matrix. The default backend is R DESeq2; --method ttest selects Welch tests. The R bridge applies apeglm or ashr shrinkage when installed, otherwise raw estimates. This is not a single-cell or splicing analysis.
Inputs & Outputs
CLI input is a gene-first CSV. The library takes a gene-indexed DataFrame. Both require nonnegative integer counts. Outputs include tables/de_results.csv, tables/de_significant.csv, four diagnostic figures, report.md and result.json; DESeq2 intermediate tables are backend-dependent.
API
<!-- api:begin generated from _api.py; regenerate with run.py api <skill dir> --write -->differential_expression(counts, *, method='deseq2', control_prefix='ctrl', treat_prefix='treat', padj_cutoff=0.05, lfc_cutoff=1.0, min_count=10)
Compare treatment against control without changing the count matrix.
:param counts: Gene-indexed DataFrame of nonnegative integer raw counts. :param method: CLI default deseq2 (R); ttest selects Welch tests. :param control_prefix: CLI default ctrl selects control columns. :param treat_prefix: CLI default treat selects treatment columns. :param padj_cutoff: CLI default 0.05; significance requires a smaller adjusted p. :param lfc_cutoff: CLI default 1.0; absolute log2 effect must exceed it. :param min_count: Legacy filtering default 10 for total counts across selected samples. :returns: DE DataFrame with effect estimates, p values and run diagnostics in attrs. :raises ValueError: Counts, method, groups or thresholds are invalid. :raises ImportError: R DESeq2 is missing; use install_skill_deps for DESeq2.
run_info(result, *, keep=True)
Read filtering, group and executed-method diagnostics.
:param result: DataFrame returned by differential_expression. :param keep: Default True; False removes diagnostics from attrs. :returns: Diagnostic dictionary, empty after removal.
volcano_figure(result)
Plot reported log2 effects and adjusted significance.
:param result: DE DataFrame with log2FoldChange and padj. :returns: A matplotlib Figure without saving files. :raises KeyError: Required columns are absent.
<!-- api:end -->Key CLI
python skills/bulkrna/bulkrna-de/bulkrna_de.py --demo --output /tmp/bulkrna-de
python skills/bulkrna/bulkrna-de/bulkrna_de.py --input counts.csv --output results/de --method ttestGotchas
run_info(result)['method_used']identifies the executed method. Missing DESeq2 raises an installation hint; a failed R fit can fall back to Welch with a warning andfallback_reason.run_info(result)['lfc_note']distinguishes Welch effects from the R bridge's package-dependent shrinkage. Welch tests are not a substitute for biological replication.run_info(result)['n_tested']counts genes after the default total-count filter of 10. Unmatched sample prefixes do not enter the comparison.
Dependencies
numpy, pandas, scipy, matplotlib, DESeq2
© 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 9 other files (references) in skills/bulkrna/bulkrna-de of TianGzlab/OmicsClaw.
- SKILL.md
- _api.py
- bulkrna_de.py
- examples/example_step.py
- references/methodology.md
- references/output_contract.md
- references/parameters.md
- tests/__init__.py
- tests/test_api.py
- tests/test_bulkrna_de.py
Open the folder on GitHubat commit 90a3bec
Compare with similar skills
Bulkrna De 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 De this skillTianGzlab/OmicsClaw | 161 | — | ~867 | 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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13C Metabolic Flux Analysis
K-Dense-AI/scientific-agent-skills
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Clinvar Database
google-deepmind/science-skills
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
aiming-lab/AutoResearchClaw
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
google-deepmind/science-skills
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.
More from TianGzlab/OmicsClaw
All 88 skills in this repoBulkrna Cosinor Rhythm
TianGzlab/OmicsClaw
Load when the user needs Deterministic fixed-period 24-hour single-component cosinor OLS rhythm analysis for a bulk RNA time-course CSV.
Bulkrna Batch Correction
TianGzlab/OmicsClaw
Load when correcting batch effects in bulk expression using R sva ComBat or the legacy Python parametric approximation.
Bulkrna Coexpression
TianGzlab/OmicsClaw
Load when discovering bulk gene co-expression modules and hub genes with R WGCNA.
Bulkrna Deconvolution
TianGzlab/OmicsClaw
Load when estimating cell-type proportions in bulk RNA-seq samples from a single-cell or signature-matrix reference.
Bulkrna Enrichment
TianGzlab/OmicsClaw
Load when running pathway / GO term enrichment on a bulk RNA-seq DE result list.
Bulkrna Geneid Mapping
TianGzlab/OmicsClaw
Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference.
Related
Categories
Questions about Bulkrna De
What does Bulkrna De do?
Load when comparing gene expression between two conditions in bulk RNA-seq count data. Bulkrna De is an agent skill from TianGzlab/OmicsClaw. Load when comparing gene expression between two conditions in bulk RNA-seq count data.
When should I use Bulkrna De?
Bulkrna De fits situations like: tasks that involve Bioinformatics.
How do I install Bulkrna De in Claude Code?
Run `npx skills add TianGzlab/OmicsClaw --skill bulkrna-de -a claude-code`. Or copy the skill folder (skills/bulkrna/bulkrna-de in TianGzlab/OmicsClaw) into .claude/skills/bulkrna-de in your project. Claude Code loads it when a task matches its description.
How do I install Bulkrna De in Codex?
Run `npx skills add TianGzlab/OmicsClaw --skill bulkrna-de -a codex`. Or copy the skill folder (skills/bulkrna/bulkrna-de in TianGzlab/OmicsClaw) into .agents/skills/bulkrna-de in your project. Codex loads it when a task matches its description.
Can I use Bulkrna De 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-de -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-de, .gemini/skills/bulkrna-de, .github/skills/bulkrna-de and .opencode/skills/bulkrna-de in your project.
What does Bulkrna De need to run?
Going by SKILL.md and its folder, Bulkrna De needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Bulkrna De 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 De 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 De use?
Bulkrna De 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 De use?
About 867 tokens (SKILL.md is roughly 3.5k 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 738 tokens, read only when the agent opens those files.
What are the alternatives to Bulkrna De?
Skills that share tags, products or a category with Bulkrna De: 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 De?
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.