scikit-bio is a skill in K-Dense-AI/scientific-agent-skills, last changed 1 Oct 2026. It can run shell commands, reach the network, name web addresses and pre-approve tools — read the findings before installing.
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
At a glance
What it can touch
How much a skill can do, not whether it is risky.
Pattern check
1 item to review
Broad tools pre-approved in allowed-tools
R34 · High · SKILL.md:5Commit a25cf9e · 3 Nov 2026
How the check worksPattern check:1 item to reviewSee it
Install
Each tab says whether it installs commit a25cf9e, the one we checked, or the latest version.
OpenCode also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Goose also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Windsurf (Devin Desktop) also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Zed also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Roo Code also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Factory Droid also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Junie also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
Amp also looks in .agents/skills/ and ~/.agents/skills/, so use the Any agent steps.
No install command here reaches Kiro. Copy the skill's folder into .kiro/skills/ in your project, or ~/.kiro/skills/ for all your projects. K-Dense-AI/scientific-agent-skills/skills/scikit-bio (opens in a new tab)
Antigravity also looks in .agents/skills/, so the Any agent steps reach it with This project. For All projects, see where Antigravity looks.
Cline also looks in .claude/skills/, so the Claude Code steps reach it with This project. For All projects, see where Cline looks.
Read this before installing: Broad tools pre-approved in allowed-tools — SKILL.md:5
Claude Code
Pinned to commit a25cf9e, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/K-Dense-AI/scientific-agent-skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&git -C "$tmp" sparse-checkout set -- skills/scikit-bio &&git -C "$tmp" checkout -q a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&mkdir -p .claude/skills &&mkdir .claude/skills/scikit-bio &&cp -R "$tmp"/skills/scikit-bio/. .claude/skills/scikit-bio/ &&rm -rf "$tmp"If Claude Code was already running and this created the skills folder, run /reload-skills.
Claude apps
Pinned to commit a25cf9e, the one we checked.
Skills in the Claude apps belong to your account rather than to a project.
Make scikit-bio.zip, with the skill folder at the top level:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/K-Dense-AI/scientific-agent-skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&git -C "$tmp" sparse-checkout set -- skills/scikit-bio &&git -C "$tmp" checkout -q a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&out="$(mktemp -d)" &&cp -R "$tmp"/skills/scikit-bio "$out"/scikit-bio &&(cd "$out" && zip -qr - scikit-bio) > scikit-bio.zip &&rm -rf "$tmp" "$out"In Claude, open Customize > Skills, select +, then + Create skill > Upload a skill, and choose scikit-bio.zip.
On Free, Pro and Max plans, turn on Code execution and file creation (Create and edit files in newer settings) under Settings > Capabilities.
Codex
Pinned to commit a25cf9e, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/K-Dense-AI/scientific-agent-skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&git -C "$tmp" sparse-checkout set -- skills/scikit-bio &&git -C "$tmp" checkout -q a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&mkdir -p .agents/skills &&mkdir .agents/skills/scikit-bio &&cp -R "$tmp"/skills/scikit-bio/. .agents/skills/scikit-bio/ &&rm -rf "$tmp"Codex picks up new skills on its own; restart it if this one does not appear.
Cursor
Pinned to commit a25cf9e, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/K-Dense-AI/scientific-agent-skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&git -C "$tmp" sparse-checkout set -- skills/scikit-bio &&git -C "$tmp" checkout -q a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&mkdir -p .cursor/skills &&mkdir .cursor/skills/scikit-bio &&cp -R "$tmp"/skills/scikit-bio/. .cursor/skills/scikit-bio/ &&rm -rf "$tmp"Copilot & VS Code
Pinned to commit a25cf9e, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/K-Dense-AI/scientific-agent-skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&git -C "$tmp" sparse-checkout set -- skills/scikit-bio &&git -C "$tmp" checkout -q a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&mkdir -p .github/skills &&mkdir .github/skills/scikit-bio &&cp -R "$tmp"/skills/scikit-bio/. .github/skills/scikit-bio/ &&rm -rf "$tmp"In a running Copilot CLI session, run /skills reload.
Or install it with gh skill, which also installs the commit we checked. Needs GitHub CLI 2.90 or later.
gh skill install K-Dense-AI/scientific-agent-skills skills/scikit-bio/SKILL.md@a25cf9ec00e2745d03f8704acf6f6919694ccd9a --agent github-copilot --scope projectGemini CLI
Pinned to commit a25cf9e, the one we checked.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/K-Dense-AI/scientific-agent-skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&git -C "$tmp" sparse-checkout set -- skills/scikit-bio &&git -C "$tmp" checkout -q a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&mkdir -p .gemini/skills &&mkdir .gemini/skills/scikit-bio &&cp -R "$tmp"/skills/scikit-bio/. .gemini/skills/scikit-bio/ &&rm -rf "$tmp"In a running session, run /skills reload.
Or use Gemini CLI’s own installer. Installs the latest version, not the one we checked.
gemini skills install https://github.com/K-Dense-AI/scientific-agent-skills.git --path skills/scikit-bio --scope workspaceAny agent
Pinned to commit a25cf9e, the one we checked.
OpenCode, Goose, Windsurf (Devin Desktop), Zed, Roo Code, Factory Droid, Junie, Amp and Antigravity read .agents/skills in a project.
From your project's root folder:
tmp="$(mktemp -d)" &&git clone -q --depth 1 --filter=blob:none --no-checkout https://github.com/K-Dense-AI/scientific-agent-skills.git "$tmp" &&git -C "$tmp" fetch -q --depth 1 origin a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&git -C "$tmp" sparse-checkout set -- skills/scikit-bio &&git -C "$tmp" checkout -q a25cf9ec00e2745d03f8704acf6f6919694ccd9a &&mkdir -p .agents/skills &&mkdir .agents/skills/scikit-bio &&cp -R "$tmp"/skills/scikit-bio/. .agents/skills/scikit-bio/ &&rm -rf "$tmp"Or use the skills CLI from skills.sh. Installs the latest version, not the one we checked. The skills CLI reports installs to skills.sh unless you set DISABLE_TELEMETRY=1.
npx skills@1.7.4 add K-Dense-AI/scientific-agent-skills --skill scikit-bioWhat it can touch
From the files and frontmatter at commit a25cf9e. This is how much a skill can do, not whether it is risky.
Pattern check
Pattern check: 1 item to review · commit a25cf9e · 3 Nov 2026
We checked every text file in this skill, at commit a25cf9e on 3 Nov 2026, against 45 published patterns such as download-and-run commands, hidden text and credential access. We don't run the skill, we don't read the web pages it points to, and we can't judge everything its instructions might lead an agent to do. In published tests, pattern checks like this one missed most malicious skills. Read the skill before you install it — especially anything it asks you to download or run.
How the check worksReport an incorrect finding
Outside links we did not follow
- https://scikit.bio/docs/latest/table.html
- https://scikit.bio/docs/latest/
- https://github.com/scikit-bio/scikit-bio
- https://github.com/scikit-bio/scikit-bio/blob/main/CHANGELOG.md
- https://www.nature.com/articles/s41592-025-02981-z
- https://forum.qiime2.org
- https://doi.org/10.48550/arXiv.2609.00065
- https://arxiv.org/abs/2609.00065
- http://export.arxiv.org/api/query?id_list=2609.00065
- https://pypi.org/pypi/scikit-bio/json
Show 29 more
- https://github.com/scikit-bio/scikit-bio/releases/tag/0.7.4
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/CHANGELOG.md
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/sequence/_sequence.py
- https://scikit.bio/docs/latest/generated/skbio.alignment.pair_align.html
- https://scikit.bio/docs/latest/generated/skbio.alignment.TabularMSA.html
- https://scikit.bio/docs/latest/generated/skbio.alignment.multi_align.html
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/tree/_tree.py
- https://scikit.bio/docs/latest/generated/skbio.tree.nj.html
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/tree/_me.py
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/diversity/_driver.py
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/diversity/_util.py
- https://scikit.bio/docs/latest/generated/skbio.stats.subsample_counts.html
- https://scikit.bio/docs/latest/generated/skbio.stats.ordination.pcoa.html
- https://scikit.bio/docs/latest/generated/skbio.stats.ordination.cca.html
- https://scikit.bio/docs/latest/generated/skbio.stats.ordination.rda.html
- https://scikit.bio/docs/latest/generated/skbio.stats.distance.mantel.html
- https://scikit.bio/docs/latest/generated/skbio.stats.distance.permdisp.html
- https://scikit.bio/docs/latest/stats.distance.html
- https://scikit.bio/docs/latest/generated/skbio.stats.composition.ancom.html
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/stats/composition/_dirmult.py
- https://scikit.bio/docs/latest/io.html
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/io/format/fasta.py
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/io/format/fastq.py
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/io/format/biom.py
- https://biom-format.org/documentation/table_objects.html
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/table/_augment.py
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/embedding/_embedding.py
- https://github.com/scikit-bio/scikit-bio/blob/0.7.4/skbio/embedding/_protein.py
- https://amplicon-docs.qiime2.org/en/latest/how-to-guides/how-to-import/
Format check
Each agent reads SKILL.md a little differently. We check the file against each one's published rules; we don't run the skill in any agent.
Agent Skills specPasses with warnings
The open format from agentskills.io, held to the strictest version of each rule among the agents we check.
- Warning
The body is about 5,805 tokens (approx.); the spec suggests under 5,000. B2
Fix: Move detail into reference files that the agent reads only when needed.
- Note
The description doesn't say when to use the skill. D6
Fix: Add a sentence such as "Use when …" naming the requests or files that should trigger it.
- Warning
Claude CodePasses
Claude Code reads its own extra fields, ignores unknown ones, and still loads a skill whose frontmatter is broken, without its fields.
- Note
The body is about 5,805 tokens (approx.); the spec suggests under 5,000. After compaction Claude Code keeps only the first 5,000 tokens of a skill. B2
Fix: Move detail into reference files that the agent reads only when needed.
- Note
Claude apps & API uploadPasses
Uploading to claude.ai or the Claude API, or packaging with Anthropic's script, accepts only the six spec fields and stops on anything else.
- Note
The body is about 5,805 tokens (approx.); the spec suggests under 5,000. Anthropic's guidance says the same. B2
Fix: Move detail into reference files that the agent reads only when needed.
- Note
- OpenAI (Codex & API)Passes
- VS Code & CopilotPasses
SKILL.md
Files
3 files
| Path | Size |
|---|---|
| SKILL.md (opens in a new tab) | 23.3 KB |
| references/api_reference.md (opens in a new tab) | 22.8 KB |
| references/review.md (opens in a new tab) | 8.5 KB |
Copies
These share its SKILL.md or its name and description but not all its files, so we list them separately.
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