PyDESeq2 Differential Expression
davila7/claude-code-templates
Runs differential gene expression analysis on bulk RNA-seq counts with PyDESeq2: design formulas, Wald tests, FDR correction and volcano or MA plots.
A skill your agent uses for OmicVerse bulk RNA-seq, enrichment/signature scoring, metabolomics, proteomics, microbiome, and statistical table workflows.
Install Multiomics Statistics
$ npx skills add VectorSpaceLab/AREX-Skill --skill multiomics-statistics -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill multiomics-statistics --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/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics .claude/skills/multiomics-statistics && 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 "multiomics-statistics" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics into .claude/skills/multiomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiomics-statistics", 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/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statisticsType 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 VectorSpaceLab/AREX-Skill --skill multiomics-statistics -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill multiomics-statistics --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics .agents/skills/multiomics-statistics && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "multiomics-statistics" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics into .agents/skills/multiomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiomics-statistics", 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 VectorSpaceLab/AREX-Skill --skill multiomics-statistics -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill multiomics-statistics --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics .cursor/skills/multiomics-statistics && 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 "multiomics-statistics" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics into .cursor/skills/multiomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiomics-statistics", 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/VectorSpaceLab/AREX-Skill.git --path skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics--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 VectorSpaceLab/AREX-Skill --skill multiomics-statistics -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill multiomics-statistics --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics .gemini/skills/multiomics-statistics && 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 "multiomics-statistics" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics into .gemini/skills/multiomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiomics-statistics", 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 VectorSpaceLab/AREX-Skill multiomics-statisticsInstalls 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 VectorSpaceLab/AREX-Skill --skill multiomics-statistics -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics .github/skills/multiomics-statistics && 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 "multiomics-statistics" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics into .github/skills/multiomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiomics-statistics", 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 VectorSpaceLab/AREX-Skill --skill multiomics-statistics -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install VectorSpaceLab/AREX-Skill multiomics-statistics --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/VectorSpaceLab/AREX-Skill.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics .opencode/skills/multiomics-statistics && 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 "multiomics-statistics" agent skill from https://github.com/VectorSpaceLab/AREX-Skill/tree/main/skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics into .opencode/skills/multiomics-statistics/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "multiomics-statistics", 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
multiomics-statistics- GitHub stars
- 330
- Token cost
- ~1k tokens
- SKILL.md length
- 384 words
- Files
- 6 (incl. scripts, references)
- Skills in repo
- 159
- Repo updated
- First seen
- Licence
- GPL-3.0
At a glance
A skill your agent uses for OmicVerse bulk RNA-seq, enrichment/signature scoring, metabolomics, proteomics, microbiome, and statistical table workflows.
- Works in 5 steps: Identify the omics family and validate… → Check sample IDs and design columns… → Choose a conservative local workflow… → …
- OmicVerse bulk RNA-seq
- SKILL.md covers When to Use, Route Elsewhere, Reference Map and Safe Operating Pattern
- Runs Python scripts from its folder; calls python
What it does
Multiomics Statistics is an agent skill from VectorSpaceLab/AREX-Skill. Use for OmicVerse bulk RNA-seq, enrichment/signature scoring, metabolomics, proteomics, microbiome, and statistical table workflows.
Its SKILL.md is about 1k 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 `references/api-reference.md`, `references/data-formats.md` and `references/statistical-workflows.md`).
It sits in Research & Science, covering Bioinformatics and Statistics. It works with Model Context Protocol and AnnData. The repository describes itself as: A Skill Library for Automated Machine Learning. The licence is GPL-3.0.
When your agent uses it
- OmicVerse bulk RNA-seq
- Enrichment/signature scoring
- Statistical table workflows
Example prompts
- “/multiomics-statistics”
Requirements
- Python 3
Workflow steps
5 steps, taken from the first numbered list in SKILL.md.
- Identify the omics family and validate orientation before loading data. Most ov.metabol, ov.protein, and ov.micro APIs expect AnnData with…
- Check sample IDs and design columns before any statistical call. Run the bundled checker for matrix-plus-metadata workflows
- Choose a conservative local workflow first. Do not assume KEGG, HMDB, ChEBI, LION, Enrichr, or other remote resources are safe or…
- Use optional backends deliberately. If pydeseq2, pymfuzz, pydeqms, pyimputelcmd, pyproda, pylipidr, pygoslin, or scikit-bio is missing…
- Keep outputs as explicit tables. Record result column semantics such as pvalue, padj, qvalue, log2FC, P.Value, adj.P.Val, score_, and…
What it can do on your machine
Read from SKILL.md and the folder at commit ac3fe1a. 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 1 file in scripts/ (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
Multiomics Statistics loads about 1k tokens when it runs, and up to ~11k if it reads all its reference files. Until then it costs about 39 tokens; SKILL.md has 384 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
The full file from VectorSpaceLab/AREX-Skill at commit ac3fe1a, republished under its GPL-3.0 licence (© VectorSpaceLab). 384 words, ~1,033 tokens.
Download SKILL.mdSave it as
.claude/skills/multiomics-statistics/SKILL.md (or your agent's skills folder). This skill also uses 5 other files; get the full folder from GitHub.- name
- multiomics-statistics
- description
- Use for OmicVerse bulk RNA-seq, enrichment/signature scoring, metabolomics, proteomics, microbiome, and statistical table workflows.
- disable-model-invocation
- true
- metadata.disco-role
- operating
- license
- GPL 3.0
Multiomics Statistics
Use this sub-skill when the task is table-centric rather than single-cell, spatial, alignment, genetics, AIRR, molecular, CLI, or MCP runtime work. Start at the root routing skill if the task crosses domains.
When to Use
- Bulk RNA-seq differential expression, offline ORA/GSEA, WGCNA-style modules, or time-course statistics with
ov.bulk. - Gene-set/signature scoring on AnnData or data frames with
ov.es.aucell,ov.es.ucell,ov.es.ora,ov.es.decouple,ov.es.decoupler, orov.es.consensus. - Metabolomics workflows from wide peak tables or MetaboAnalyst-style CSVs through QC, normalization, differential testing, PLS-DA, pathway enrichment, and biomarker panels.
- Proteomics workflows from MaxQuant, DIA-NN, FragPipe, Olink, or wide intensity tables through QC, normalization, imputation, and differential testing.
- Microbiome workflows using samples-by-taxa AnnData for alpha/beta diversity, ordination, differential abundance, meta-analysis, and paired microbe-metabolite statistics.
Route Elsewhere
- AnnData file reading, general preprocessing, plotting basics, report/provenance, and registry discovery:
../core-analysis/SKILL.md. - Single-cell annotation, marker ranking, trajectory, velocity, cell communication, pseudobulk, and batch integration:
../single-cell-workflows/SKILL.md. - GWAS, eQTL, AIRR, molecular structure, raw FASTQ alignment, and external binary workflows:
../specialist-domains/SKILL.md. - Exposing analyses through the CLI, registry, MCP, JARVIS, or gateway runtime:
../agentic-and-mcp/SKILL.md.
Reference Map
references/statistical-workflows.md: task recipes and validation checkpoints for bulk, enrichment, metabolomics, proteomics, and microbiome workflows.references/api-reference.md: compact API names, signatures, outputs, and optional backend mapping.references/data-formats.md: expected table orientations, AnnData slots, signature/network formats, and design metadata columns.references/troubleshooting.md: errors, optional dependency messages, network-fetcher caveats, and repair actions.scripts/check_multiomics_table.py: safe CSV/TSV schema checker for feature-by-sample matrices and sample metadata.
Show full SKILL.md (164 more words)Show less
Safe Operating Pattern
Identify the omics family and validate orientation before loading data. Most
ov.metabol,ov.protein, andov.microAPIs expectAnnDatawith samples in rows and features in columns; manyov.bulk.pyDEGinputs use genes in rows and samples in columns.Check sample IDs and design columns before any statistical call. Run the bundled checker for matrix-plus-metadata workflows:
bash python sub-skills/multiomics-statistics/scripts/check_multiomics_table.py matrix.tsv --metadata metadata.tsv --sample-id-column sample --required-metadata-cols group,batchChoose a conservative local workflow first. Do not assume KEGG, HMDB, ChEBI, LION, Enrichr, or other remote resources are safe or available unless the user explicitly authorizes network access.
Use optional backends deliberately. If
pydeseq2,pymfuzz,pydeqms,pyimputelcmd,pyproda,pylipidr,pygoslin, orscikit-biois missing, either install the narrow extra required by the workflow or switch to a pure-Python fallback documented in the API reference.Keep outputs as explicit tables. Record result column semantics such as
pvalue,padj,qvalue,log2FC,P.Value,adj.P.Val,score_<method>, andpadj_<method>before handing off to plotting or reporting.
© VectorSpaceLab, GPL-3.0. 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 5 other files (scripts, references) in skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics of VectorSpaceLab/AREX-Skill.
- SKILL.md
- references/api-reference.md
- references/data-formats.md
- references/statistical-workflows.md
- references/troubleshooting.md
- scripts/check_multiomics_table.py
Open the folder on GitHubat commit ac3fe1a
Compare with similar skills
Multiomics Statistics 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 |
|---|---|---|---|---|---|---|
| Multiomics Statistics this skillVectorSpaceLab/AREX-Skill | 330 | — | ~1k | Automated safety check: Pass | GPL-3.0 | |
| PyDESeq2 Differential Expressiondavila7/claude-code-templates | 32k | 11 repos | ~4k | Automated safety check: Pass | MIT | |
| Scanpy Single-Cell Analysisdavila7/claude-code-templates | 32k | 15 repos | ~2.8k | Automated safety check: Pass | MIT | |
| Single-Cell Initial AnalysisLigphiDonk/Oh-my--paper | 738 | 1 repos | ~1.4k | Automated safety check: Pass | MIT | |
| Ukb Ppp Region FetchClawBio/ClawBio | 1.2k | — | ~4.6k | Automated safety check: Pass | MIT | |
| Volcano Plot Scriptaipoch/medical-research-skills | 2k | — | ~2.5k | Automated safety check: Pass | MIT |
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Scanpy Single-Cell Analysis
davila7/claude-code-templates
Walks through single-cell RNA-seq analysis with Scanpy: loading .h5ad and 10X data, QC, normalization, PCA and UMAP, Leiden clustering, marker genes and cell type annotation.
Single-Cell Initial Analysis
LigphiDonk/Oh-my--paper
Runs a seven-step quality-control and exploration pipeline on scRNA-seq, CyTOF or flow cytometry data and writes a plain-language report of what it found.
Ukb Ppp Region Fetch
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Fetch a regional slice of plasma pQTL summary statistics from the UK Biobank Pharma Proteomics Project (UKB-PPP; Sun 2023 Nature) for a specific (protein, ancestry) measurement.
Volcano Plot Script
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Generate R/Python code for volcano plots from DEG (Differentially Expressed Genes) analysis results.
Tooluniverse Epigenomics
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Production-ready genomics and epigenomics data processing for BixBench questions.
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Related
Works with
Categories
Questions about Multiomics Statistics
What does Multiomics Statistics do?
A skill your agent uses for OmicVerse bulk RNA-seq, enrichment/signature scoring, metabolomics, proteomics, microbiome, and statistical table workflows. Multiomics Statistics is an agent skill from VectorSpaceLab/AREX-Skill. Use for OmicVerse bulk RNA-seq, enrichment/signature scoring, metabolomics, proteomics, microbiome, and statistical table workflows.
When should I use Multiomics Statistics?
Multiomics Statistics fits situations like: omicVerse bulk RNA-seq; enrichment/signature scoring; statistical table workflows.
How do I install Multiomics Statistics in Claude Code?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill multiomics-statistics -a claude-code`. Or copy the skill folder (skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics in VectorSpaceLab/AREX-Skill) into .claude/skills/multiomics-statistics in your project. Claude Code loads it when a task matches its description.
How do I install Multiomics Statistics in Codex?
Run `npx skills add VectorSpaceLab/AREX-Skill --skill multiomics-statistics -a codex`. Or copy the skill folder (skills/repositories/repo-skills/omicverse/sub-skills/multiomics-statistics in VectorSpaceLab/AREX-Skill) into .agents/skills/multiomics-statistics in your project. Codex loads it when a task matches its description.
Can I use Multiomics Statistics 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 VectorSpaceLab/AREX-Skill --skill multiomics-statistics -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/multiomics-statistics, .gemini/skills/multiomics-statistics, .github/skills/multiomics-statistics and .opencode/skills/multiomics-statistics in your project.
What does Multiomics Statistics need to run?
Going by SKILL.md and its folder, Multiomics Statistics needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.
Does Multiomics Statistics 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 Multiomics Statistics 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 Multiomics Statistics use?
Multiomics Statistics is published under the GPL-3.0 licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.
How many tokens does Multiomics Statistics use?
About 1k tokens (SKILL.md is roughly 4.1k 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 10k tokens, read only when the agent opens those files.
What are the alternatives to Multiomics Statistics?
Skills that share tags, products or a category with Multiomics Statistics: PyDESeq2 Differential Expression (davila7/claude-code-templates, 32k stars), Scanpy Single-Cell Analysis (davila7/claude-code-templates, 32k stars), Single-Cell Initial Analysis (LigphiDonk/Oh-my--paper, 738 stars) and Ukb Ppp Region Fetch (ClawBio/ClawBio, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Multiomics Statistics?
VectorSpaceLab (a GitHub organization) maintains it in VectorSpaceLab/AREX-Skill, which has 330 GitHub stars. The repository holds 159 skills in this directory. The repository was last updated on September 3, 2026.
Source: VectorSpaceLab/AREX-Skill on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.