Gwas Database
davila7/claude-code-templates
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. An agent skill from davila7/claude-code-templates.
This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and…
Install Bioconductor Ptairms
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ptairms -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-ptairms --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/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/transcriptomics/ptairms .claude/skills/bioconductor-ptairms && 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 "bioconductor-ptairms" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ptairms into .claude/skills/bioconductor-ptairms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ptairms", 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/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ptairmsType 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ptairms -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-ptairms --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/transcriptomics/ptairms .agents/skills/bioconductor-ptairms && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bioconductor-ptairms" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ptairms into .agents/skills/bioconductor-ptairms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ptairms", 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ptairms -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-ptairms --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/transcriptomics/ptairms .cursor/skills/bioconductor-ptairms && 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 "bioconductor-ptairms" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ptairms into .cursor/skills/bioconductor-ptairms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ptairms", 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/bioMate-AI/biomate-bioconductor-kb.git --path skills/transcriptomics/ptairms--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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ptairms -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-ptairms --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/transcriptomics/ptairms .gemini/skills/bioconductor-ptairms && 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 "bioconductor-ptairms" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ptairms into .gemini/skills/bioconductor-ptairms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ptairms", 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 bioMate-AI/biomate-bioconductor-kb bioconductor-ptairmsInstalls 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ptairms -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/transcriptomics/ptairms .github/skills/bioconductor-ptairms && 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 "bioconductor-ptairms" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ptairms into .github/skills/bioconductor-ptairms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ptairms", 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ptairms -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-ptairms --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/bioMate-AI/biomate-bioconductor-kb.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/transcriptomics/ptairms .opencode/skills/bioconductor-ptairms && 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 "bioconductor-ptairms" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ptairms into .opencode/skills/bioconductor-ptairms/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ptairms", 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
bioconductor-ptairms- GitHub stars
- 804
- Token cost
- ~1.5k tokens
- SKILL.md length
- 542 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and…
- Works in 4 steps: Read the raw file using readRaw (exactly… → Perform calibration on the single raw… → Determine time limits… → …
- Tasks that involve Performance reviews
- SKILL.md covers Workflows, When to Use, When NOT to Use and Data Requirements, plus 6 more sections
- Instructions only: no scripts, shell commands, URLs or credentials in SKILL.md
What it does
Bioconductor Ptairms is an agent skill from bioMate-AI/biomate-bioconductor-kb. This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis). This package also permit usefull tools for cohorts management as analyzing data progressively, visualization tools and quality control. The steps include calibration, expiration detection, peak detection and qua
Its SKILL.md is about 1.5k tokens, which your agent loads only when the skill is triggered. It is a single SKILL.md file with no bundled scripts.
It sits in Data & Analytics, covering Performance reviews, Data analysis and Statistics. The repository describes itself as: BioMate-KB Bioconductor Skills — 200 packages (top 100 by downloads + 100 rising stars) as vignette-grounded Claude/agent skills, with per-package workflow recipes.
When your agent uses it
- Tasks that involve Performance reviews
- Tasks that involve Data analysis
- Tasks that involve Statistics
Example prompts
- “sample by features”
- “/bioconductor-ptairms”
Workflow steps
4 steps, taken from the first numbered list in SKILL.md.
- Read the raw file using readRaw (exactly as documented)
- Perform calibration on the single raw object
- Determine time limits (expiration/headspace limits)
- Write named output files for the meaningful results
What it can do on your machine
Read from SKILL.md and the folder at commit c9bd4d8. 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
No scripts in the folder and no shell commands in SKILL.md (its code samples are r).
From the folder's file list and the shell code blocks in SKILL.md.
Network
Links to these hosts (documentation or services it may open):
bioconductor.org
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
Bioconductor Ptairms loads about 1.5k tokens when it runs. Until then it costs about 130 tokens; SKILL.md has 542 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
Its licence (Custom licence) doesn't allow us to republish the file, so here is its outline and opening line. It has 542 words (~1,524 tokens).
“Preprocess a directory of raw PTR-TOF-MS HDF5 files to calibrate, detect peaks, align samples, impute missing values, annotate VOCs, and export an ExpressionSet.”
- name
- bioconductor-ptairms
- when_to_use
- Use when: ptaiMS: Processing and analysis of PTR-TOF-MS data; Metabolomics data analysis (ptairMS). Not for: Requires R ≥ 4.0.0 and Bioconductor ≥ 3.16
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/ptairms of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Ptairms 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 |
|---|---|---|---|---|---|---|
| Bioconductor Ptairms this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.5k | Automated safety check: Pass | Custom licence | |
| Gwas Databasedavila7/claude-code-templates | 33k | 10 repos | ~5k | Automated safety check: Pass | MIT | |
| Ukb Ppp Region FetchClawBio/ClawBio | 1.2k | — | ~4.6k | Automated safety check: Pass | MIT | |
| Progressive Estimationsickn33/agentic-awesome-skills | 47k | 2 repos | ~863 | Automated safety check: Pass | MIT | |
| Bio Metabolomics Targeted AnalysisGPTomics/bioSkills | 1.2k | 1 repos | ~5.1k | Automated safety check: Pass | MIT | |
| Bio Population Genetics Linkage DisequilibriumGPTomics/bioSkills | 1.2k | 1 repos | ~4.7k | Automated safety check: Pass | MIT |
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Related
Categories
Questions about Bioconductor Ptairms
What does Bioconductor Ptairms do?
This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and…. Bioconductor Ptairms is an agent skill from bioMate-AI/biomate-bioconductor-kb. This package implements a suite of methods to preprocess data from PTR-TOF-MS instruments (HDF5 format) and generates the 'sample by features' table of peak intensities in addition to the sample and feature metadata (as a single ExpressionSet object for subsequent statistical analysis).
When should I use Bioconductor Ptairms?
Bioconductor Ptairms fits situations like: tasks that involve Performance reviews; tasks that involve Data analysis; tasks that involve Statistics.
How do I install Bioconductor Ptairms in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ptairms -a claude-code`. Or copy the skill folder (skills/transcriptomics/ptairms in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-ptairms in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Ptairms in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ptairms -a codex`. Or copy the skill folder (skills/transcriptomics/ptairms in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-ptairms in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Ptairms 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 bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ptairms -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bioconductor-ptairms, .gemini/skills/bioconductor-ptairms, .github/skills/bioconductor-ptairms and .opencode/skills/bioconductor-ptairms in your project.
What does Bioconductor Ptairms need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Ptairms is instructions for the agent only.
Does Bioconductor Ptairms access the network?
SKILL.md names 1 domain. As links in the text: bioconductor.org. This is read from the text; nothing was executed.
Is Bioconductor Ptairms 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 Bioconductor Ptairms use?
Bioconductor Ptairms has a licence file (the repository's licence) that doesn't match a standard licence. Read it on GitHub before reusing the skill.
How many tokens does Bioconductor Ptairms use?
About 1.5k tokens (SKILL.md is roughly 6.1k 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 Bioconductor Ptairms?
Skills that share tags, products or a category with Bioconductor Ptairms: Gwas Database (davila7/claude-code-templates, 33k stars), Ukb Ppp Region Fetch (ClawBio/ClawBio, 1.2k stars), Progressive Estimation (sickn33/agentic-awesome-skills, 47k stars) and Bio Metabolomics Targeted Analysis (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Ptairms?
bioMate-AI (a GitHub organization) maintains it in bioMate-AI/biomate-bioconductor-kb, which has 804 GitHub stars. The repository holds 112 skills in this directory. The repository was last updated on June 20, 2026.
Source: bioMate-AI/biomate-bioconductor-kb on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.