Stata C Plugins
dylantmoore/stata-skill
Develop high-performance C/C++ plugins for Stata using the stplugin.h SDK.
This packages provides C++ header files for developers wishing to create R packages that processes BAM files.
Install Bioconductor Ompbam
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ompbam -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-ompbam --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/ompbam .claude/skills/bioconductor-ompbam && 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-ompbam" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ompbam into .claude/skills/bioconductor-ompbam/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ompbam", 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/ompbamType 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-ompbam -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-ompbam --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/ompbam .agents/skills/bioconductor-ompbam && 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-ompbam" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ompbam into .agents/skills/bioconductor-ompbam/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ompbam", 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-ompbam -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-ompbam --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/ompbam .cursor/skills/bioconductor-ompbam && 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-ompbam" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ompbam into .cursor/skills/bioconductor-ompbam/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ompbam", 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/ompbam--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-ompbam -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-ompbam --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/ompbam .gemini/skills/bioconductor-ompbam && 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-ompbam" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ompbam into .gemini/skills/bioconductor-ompbam/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ompbam", 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-ompbamInstalls 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-ompbam -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/ompbam .github/skills/bioconductor-ompbam && 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-ompbam" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ompbam into .github/skills/bioconductor-ompbam/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ompbam", 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-ompbam -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-ompbam --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/ompbam .opencode/skills/bioconductor-ompbam && 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-ompbam" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/ompbam into .opencode/skills/bioconductor-ompbam/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-ompbam", 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-ompbam- GitHub stars
- 804
- Token cost
- ~993 tokens
- SKILL.md length
- 377 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
This packages provides C++ header files for developers wishing to create R packages that processes BAM files.
- Tasks that involve Tutoring and explanations
- SKILL.md covers Workflows, When to Use, When NOT to Use and Data Requirements, plus 6 more sections
- Calls brew
- Tasks that involve Bioinformatics
What it does
Bioconductor Ompbam is an agent skill from bioMate-AI/biomate-bioconductor-kb. This packages provides C++ header files for developers wishing to create R packages that processes BAM files. ompBAM automates file access, memory management, and handling of multiple threads 'behind the scenes', so developers can focus on creating domain-specific functionality. The included vignette contains detailed documentation of this API, including quick-start instructions to create a new ompBAM-based package, and step-by-step explanation of the functionality behind the example packaged in
Its SKILL.md is about 990 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 Research & Science, covering Tutoring and explanations and Bioinformatics. It works with C++ and macOS. 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 Tutoring and explanations
- Tasks that involve Bioinformatics
Example prompts
- “behind the scenes”
- “/bioconductor-ompbam”
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
Shell commands in SKILL.md call:
brew
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 Ompbam loads about 993 tokens when it runs. Until then it costs about 130 tokens; SKILL.md has 377 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 377 words (~993 tokens).
“Input: A destination directory path for the new package. Output: A fully configured R package directory structure containing C++ templates and configuration files linked to ompBAM.”
- name
- bioconductor-ompbam
- when_to_use
- Use when: This packages provides C++ header files for developers wishing to create R packages that processes BAM files; ompBAM API Documentation; Single-cell…
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/ompbam of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Ompbam 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 Ompbam this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~993 | Automated safety check: Pass | Custom licence | |
| Stata C Pluginsdylantmoore/stata-skill | 291 | 1 repos | ~5.8k | Automated safety check: Pass | Custom licence | |
| Tbtoolsxuzhougeng/wispterm | 442 | — | ~2.3k | Automated safety check: Pass | MIT | |
| TiledbvcfK-Dense-AI/scientific-agent-skills | 48k | 1 repos | ~3.5k | Automated safety check: Pass | MIT | |
| Bio Ecological Genomics Species DelimitationGPTomics/bioSkills | 1.2k | 1 repos | ~6.6k | Automated safety check: Pass | MIT | |
| JS Cpp Protocolnotepadqq/notepadqq | 2.3k | — | ~3.2k | Automated safety check: Pass | GPL-3.0 |
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Related
Categories
Questions about Bioconductor Ompbam
What does Bioconductor Ompbam do?
This packages provides C++ header files for developers wishing to create R packages that processes BAM files. Bioconductor Ompbam is an agent skill from bioMate-AI/biomate-bioconductor-kb. This packages provides C++ header files for developers wishing to create R packages that processes BAM files.
When should I use Bioconductor Ompbam?
Bioconductor Ompbam fits situations like: tasks that involve Tutoring and explanations; tasks that involve Bioinformatics.
How do I install Bioconductor Ompbam in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ompbam -a claude-code`. Or copy the skill folder (skills/transcriptomics/ompbam in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-ompbam in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Ompbam in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-ompbam -a codex`. Or copy the skill folder (skills/transcriptomics/ompbam in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-ompbam in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Ompbam 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-ompbam -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-ompbam, .gemini/skills/bioconductor-ompbam, .github/skills/bioconductor-ompbam and .opencode/skills/bioconductor-ompbam in your project.
What does Bioconductor Ompbam need to run?
Going by SKILL.md and its folder, Bioconductor Ompbam needs the command-line tools its instructions call (brew).
Does Bioconductor Ompbam 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 Ompbam 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 Ompbam use?
Bioconductor Ompbam 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 Ompbam use?
About 993 tokens (SKILL.md is roughly 4k 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 Ompbam?
Skills that share tags, products or a category with Bioconductor Ompbam: Stata C Plugins (dylantmoore/stata-skill, 291 stars), Tbtools (xuzhougeng/wispterm, 442 stars), Tiledbvcf (K-Dense-AI/scientific-agent-skills, 48k stars) and Bio Ecological Genomics Species Delimitation (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 Ompbam?
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.