Exploratory Data Analysis
spacering-net/codeg
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.
Agent skill
Bio Copy Number Cnvkit Analysis
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Detect copy number variants from targeted/exome sequencing using CNVkit.
No licenceAuto-check passed
Install Bio Copy Number Cnvkit Analysis
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-copy-number-cnvkit-analysis --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/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-copy-number-cnvkit-analysis .claude/skills/bio-copy-number-cnvkit-analysis && 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 "bio-copy-number-cnvkit-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-cnvkit-analysis into .claude/skills/bio-copy-number-cnvkit-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-copy-number-cnvkit-analysis", 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/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-cnvkit-analysisType 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-copy-number-cnvkit-analysis --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-copy-number-cnvkit-analysis .agents/skills/bio-copy-number-cnvkit-analysis && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-copy-number-cnvkit-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-cnvkit-analysis into .agents/skills/bio-copy-number-cnvkit-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-copy-number-cnvkit-analysis", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-copy-number-cnvkit-analysis --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-copy-number-cnvkit-analysis .cursor/skills/bio-copy-number-cnvkit-analysis && 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 "bio-copy-number-cnvkit-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-cnvkit-analysis into .cursor/skills/bio-copy-number-cnvkit-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-copy-number-cnvkit-analysis", 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/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-copy-number-cnvkit-analysis--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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-copy-number-cnvkit-analysis --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-copy-number-cnvkit-analysis .gemini/skills/bio-copy-number-cnvkit-analysis && 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 "bio-copy-number-cnvkit-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-cnvkit-analysis into .gemini/skills/bio-copy-number-cnvkit-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-copy-number-cnvkit-analysis", 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 FreedomIntelligence/OpenClaw-Medical-Skills bio-copy-number-cnvkit-analysisInstalls 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-copy-number-cnvkit-analysis .github/skills/bio-copy-number-cnvkit-analysis && 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 "bio-copy-number-cnvkit-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-cnvkit-analysis into .github/skills/bio-copy-number-cnvkit-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-copy-number-cnvkit-analysis", 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-copy-number-cnvkit-analysis --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-copy-number-cnvkit-analysis .opencode/skills/bio-copy-number-cnvkit-analysis && 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 "bio-copy-number-cnvkit-analysis" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-copy-number-cnvkit-analysis into .opencode/skills/bio-copy-number-cnvkit-analysis/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-copy-number-cnvkit-analysis", 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
bio-copy-number-cnvkit-analysis- GitHub stars
- 3.1k
- Token cost
- ~2.4k tokens
- SKILL.md length
- 546 words
- Files
- 3
- Skills in repo
- 279
- Repo updated
- First seen
- Licence
- None found
At a glance
Detect copy number variants from targeted/exome sequencing using CNVkit.
- Detecting CNVs from WES
- SKILL.md covers Version Compatibility, Basic Workflow, Build Reference from Normal… and Flat Reference (No Matched…, plus 12 more sections
- Runs Shell scripts from its folder; calls pip
- Targeted panel sequencing data
What it does
Bio Copy Number Cnvkit Analysis is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Detect copy number variants from targeted/exome sequencing using CNVkit. Supports tumor-normal pairs, tumor-only, and germline CNV calling. Use when detecting CNVs from WES or targeted panel sequencing data.
Its SKILL.md is about 2.4k tokens, which your agent loads only when the skill is triggered. The skill folder holds 3 other files (for example `examples/run_cnvkit.sh` and `usage-guide.md`).
The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Detecting CNVs from WES
- Targeted panel sequencing data
Example prompts
- “/bio-copy-number-cnvkit-analysis”
Requirements
- Python 3
- A Bash shell
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. 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 (Shell), which the agent can run.
Shell commands in SKILL.md call:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
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
Bio Copy Number Cnvkit Analysis loads about 2.4k tokens when it runs. Until then it costs about 60 tokens; SKILL.md has 546 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
Without a licence we can't republish the file, so here is its outline and opening line. It has 546 words (~2,371 tokens).
“Reference examples tested with: GATK 4.5+, bedtools 2.31+”
- name
- bio-copy-number-cnvkit-analysis
- tool_type
- cli
- primary_tool
- cnvkit
Files
SKILL.md and 2 other files in skills/bio-copy-number-cnvkit-analysis of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/run_cnvkit.sh
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Compare with similar skills
Bio Copy Number Cnvkit Analysis 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 |
|---|---|---|---|---|---|---|
| Bio Copy Number Cnvkit Analysis this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~2.4k | Automated safety check: Pass | None | |
| Exploratory Data Analysisspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Pass | MIT | |
| 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 |
Similar skills
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.
13C Metabolic Flux Analysis
K-Dense-AI/scientific-agent-skills
Estimates reaction fluxes inside cells from steady-state carbon-13 labeling data with a bundled mfapy-based solver, and reports which fluxes the data pin down.
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.
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Questions about Bio Copy Number Cnvkit Analysis
What does Bio Copy Number Cnvkit Analysis do?
Detect copy number variants from targeted/exome sequencing using CNVkit. Bio Copy Number Cnvkit Analysis is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Detect copy number variants from targeted/exome sequencing using CNVkit.
When should I use Bio Copy Number Cnvkit Analysis?
Bio Copy Number Cnvkit Analysis fits situations like: detecting CNVs from WES; targeted panel sequencing data.
How do I install Bio Copy Number Cnvkit Analysis in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis -a claude-code`. Or copy the skill folder (skills/bio-copy-number-cnvkit-analysis in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-copy-number-cnvkit-analysis in your project. Claude Code loads it when a task matches its description.
How do I install Bio Copy Number Cnvkit Analysis in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis -a codex`. Or copy the skill folder (skills/bio-copy-number-cnvkit-analysis in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-copy-number-cnvkit-analysis in your project. Codex loads it when a task matches its description.
Can I use Bio Copy Number Cnvkit Analysis 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 FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-copy-number-cnvkit-analysis -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-copy-number-cnvkit-analysis, .gemini/skills/bio-copy-number-cnvkit-analysis, .github/skills/bio-copy-number-cnvkit-analysis and .opencode/skills/bio-copy-number-cnvkit-analysis in your project.
What does Bio Copy Number Cnvkit Analysis need to run?
Going by SKILL.md and its folder, Bio Copy Number Cnvkit Analysis needs a shell for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3; A Bash shell.
Does Bio Copy Number Cnvkit Analysis access the network?
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Bio Copy Number Cnvkit Analysis 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 Bio Copy Number Cnvkit Analysis use?
No licence was found for Bio Copy Number Cnvkit Analysis or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Copy Number Cnvkit Analysis use?
About 2.4k tokens (SKILL.md is roughly 9.5k 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 Bio Copy Number Cnvkit Analysis?
Skills that share tags, products or a category with Bio Copy Number Cnvkit Analysis: Exploratory Data Analysis (spacering-net/codeg, 3.9k stars), Alphagenome Single Variant Analysis (google-deepmind/science-skills, 3.2k stars), 13C Metabolic Flux Analysis (K-Dense-AI/scientific-agent-skills, 48k stars) and Clinvar Database (google-deepmind/science-skills, 3.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Copy Number Cnvkit Analysis?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,053 GitHub stars. The repository holds 279 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.