Bulkrna Geneid Mapping
TianGzlab/OmicsClaw
Load when converting Ensembl, Entrez or symbol IDs in a bulk RNA count matrix using an explicit mapping or a small human demo reference.
In recent years a wealth of biological data has become available in public data repositories.
Install Bioconductor Biomart
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-biomart -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-biomart --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/annotation/biomart .claude/skills/bioconductor-biomart && 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-biomart" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/annotation/biomart into .claude/skills/bioconductor-biomart/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-biomart", 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/annotation/biomartType 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-biomart -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-biomart --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/annotation/biomart .agents/skills/bioconductor-biomart && 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-biomart" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/annotation/biomart into .agents/skills/bioconductor-biomart/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-biomart", 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-biomart -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-biomart --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/annotation/biomart .cursor/skills/bioconductor-biomart && 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-biomart" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/annotation/biomart into .cursor/skills/bioconductor-biomart/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-biomart", 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/annotation/biomart--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-biomart -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-biomart --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/annotation/biomart .gemini/skills/bioconductor-biomart && 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-biomart" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/annotation/biomart into .gemini/skills/bioconductor-biomart/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-biomart", 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-biomartInstalls 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-biomart -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/annotation/biomart .github/skills/bioconductor-biomart && 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-biomart" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/annotation/biomart into .github/skills/bioconductor-biomart/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-biomart", 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-biomart -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-biomart --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/annotation/biomart .opencode/skills/bioconductor-biomart && 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-biomart" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/annotation/biomart into .opencode/skills/bioconductor-biomart/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-biomart", 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-biomart- GitHub stars
- 804
- Token cost
- ~4.5k tokens
- SKILL.md length
- 1,656 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
In recent years a wealth of biological data has become available in public data repositories.
- Tasks that involve Data analysis
- SKILL.md covers Dependencies & Environment, When to Use, Do NOT Use When and Data Requirements, plus 10 more sections
- Reaches grch37.ensembl.org and sep2025.archive.ensembl.org
- Tasks that involve Bioinformatics
What it does
Bioconductor Biomart is an agent skill from bioMate-AI/biomate-bioconductor-kb. In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. bio
Its SKILL.md is about 4.5k 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 Data analysis and Bioinformatics. It works with Ensembl and NCBI. 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 Data analysis
- Tasks that involve Bioinformatics
Example prompts
- “/bioconductor-biomart”
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
Hosts in commands or code, which the agent is likely to contact:
grch37.ensembl.orgsep2025.archive.ensembl.orgmay2025.archive.ensembl.orgoct2024.archive.ensembl.orgmay2024.archive.ensembl.orgjan2024.archive.ensembl.orgjul2023.archive.ensembl.orgfeb2023.archive.ensembl.orgoct2022.archive.ensembl.orgjul2022.archive.ensembl.org
Also links to:
bioconductor.orgbiomate.aipubmed.ncbi.nlm.nih.govensembl.orgsupport.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 Biomart loads about 4.5k tokens when it runs. Until then it costs about 65 tokens; SKILL.md has 1,656 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 1,656 words (~4,523 tokens).
“Query Ensembl BioMart databases to retrieve gene annotations, ID conversions, sequence retrieval, and cross-species homology information.”
- name
- bioconductor-biomart
- when_to_use
- Use when: Convert between gene IDs (Ensembl → HGNC symbol → Entrez → RefSeq); Retrieve gene coordinates, GO terms, pathway annotations; Get protein sequences…
- user-invocable
- false
Files
Just SKILL.md in skills/annotation/biomart of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Biomart 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 Biomart this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~4.5k | Automated safety check: Pass | Custom licence | |
| Bulkrna Geneid MappingTianGzlab/OmicsClaw | 161 | — | ~1.2k | Automated safety check: Pass | Apache-2.0 | |
| Exploratory Data Analysisspacering-net/codeg | 3.9k | 14 repos | ~3.6k | Automated safety check: Pass | MIT | |
| Pyopenmsdavila7/claude-code-templates | 33k | 11 repos | ~1.4k | Automated safety check: Pass | MIT | |
| Gwas Databasedavila7/claude-code-templates | 33k | 10 repos | ~5k | Automated safety check: Pass | MIT | |
| Tooluniverse Phylogeneticswu-yc/LabClaw | 1.1k | 2 repos | ~4.2k | Automated safety check: Pass | None |
Similar skills
Exploratory Data Analysis
spacering-net/codeg
Perform comprehensive exploratory data analysis on scientific data files across 200+ file formats.
Pyopenms
davila7/claude-code-templates
Python interface to OpenMS for mass spectrometry data analysis.
Gwas Database
davila7/claude-code-templates
Query NHGRI-EBI GWAS Catalog for SNP-trait associations. An agent skill from davila7/claude-code-templates.
Tooluniverse Phylogenetics
wu-yc/LabClaw
Production-ready phylogenetics and sequence analysis skill for alignment processing, tree analysis, and evolutionary metrics.
Bio Data Visualization Manhattan Qq Locuszoom
GPTomics/bioSkills
Build Manhattan, Miami, QQ, and locuszoom-style regional plots from GWAS, TWAS, PWAS, and QTL summary statistics with correct genomic-inflation diagnostics, multi-trait overlays, lead-SNP labeling…
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This package provides a client for the Bioconductor AnnotationHub web resource.
Bioconductor Asurat
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Bioconductor Awst
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We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples.
Bioconductor Bandle
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The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data.
Bioconductor Batchelor
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Implements a variety of methods for batch correction of single-cell (RNA sequencing) data.
Bioconductor Beer
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BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data.
Related
Categories
Questions about Bioconductor Biomart
What does Bioconductor Biomart do?
In recent years a wealth of biological data has become available in public data repositories. Bioconductor Biomart is an agent skill from bioMate-AI/biomate-bioconductor-kb. In recent years a wealth of biological data has become available in public data repositories.
When should I use Bioconductor Biomart?
Bioconductor Biomart fits situations like: tasks that involve Data analysis; tasks that involve Bioinformatics.
How do I install Bioconductor Biomart in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-biomart -a claude-code`. Or copy the skill folder (skills/annotation/biomart in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-biomart in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Biomart in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-biomart -a codex`. Or copy the skill folder (skills/annotation/biomart in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-biomart in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Biomart 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-biomart -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-biomart, .gemini/skills/bioconductor-biomart, .github/skills/bioconductor-biomart and .opencode/skills/bioconductor-biomart in your project.
What does Bioconductor Biomart need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Biomart is instructions for the agent only.
Does Bioconductor Biomart access the network?
SKILL.md names 15 domains. In commands or code: grch37.ensembl.org, sep2025.archive.ensembl.org, may2025.archive.ensembl.org, oct2024.archive.ensembl.org, may2024.archive.ensembl.org, jan2024.archive.ensembl.org, jul2023.archive.ensembl.org, feb2023.archive.ensembl.org, oct2022.archive.ensembl.org and jul2022.archive.ensembl.org; the agent is likely to contact these when it follows the instructions. As links in the text: bioconductor.org, biomate.ai, pubmed.ncbi.nlm.nih.gov, ensembl.org and support.bioconductor.org. This is read from the text; nothing was executed.
Is Bioconductor Biomart 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 Biomart use?
Bioconductor Biomart 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 Biomart use?
About 4.5k tokens (SKILL.md is roughly 18k 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 Biomart?
Skills that share tags, products or a category with Bioconductor Biomart: Bulkrna Geneid Mapping (TianGzlab/OmicsClaw, 161 stars), Exploratory Data Analysis (spacering-net/codeg, 3.9k stars), Pyopenms (davila7/claude-code-templates, 33k stars) and Gwas Database (davila7/claude-code-templates, 33k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Biomart?
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.