Bio Motif Search
GPTomics/bioSkills
Find sequence motifs, degenerate IUPAC patterns, and transcription-factor binding sites in DNA/RNA using Biopython and regex, including position weight matrix (PWM/PSSM) scoring.
This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype.
Install Bioconductor Cageminer
$ npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-cageminer -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-cageminer --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/cageminer .claude/skills/bioconductor-cageminer && 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-cageminer" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/cageminer into .claude/skills/bioconductor-cageminer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-cageminer", 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/cageminerType 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-cageminer -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-cageminer --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/cageminer .agents/skills/bioconductor-cageminer && 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-cageminer" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/cageminer into .agents/skills/bioconductor-cageminer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-cageminer", 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-cageminer -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-cageminer --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/cageminer .cursor/skills/bioconductor-cageminer && 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-cageminer" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/cageminer into .cursor/skills/bioconductor-cageminer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-cageminer", 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/cageminer--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-cageminer -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install bioMate-AI/biomate-bioconductor-kb bioconductor-cageminer --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/cageminer .gemini/skills/bioconductor-cageminer && 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-cageminer" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/cageminer into .gemini/skills/bioconductor-cageminer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-cageminer", 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-cageminerInstalls 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-cageminer -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/cageminer .github/skills/bioconductor-cageminer && 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-cageminer" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/cageminer into .github/skills/bioconductor-cageminer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-cageminer", 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-cageminer -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-cageminer --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/cageminer .opencode/skills/bioconductor-cageminer && 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-cageminer" agent skill from https://github.com/bioMate-AI/biomate-bioconductor-kb/tree/main/skills/transcriptomics/cageminer into .opencode/skills/bioconductor-cageminer/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bioconductor-cageminer", 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-cageminer- GitHub stars
- 804
- Token cost
- ~1.3k tokens
- SKILL.md length
- 379 words
- Files
- 1
- Skills in repo
- 112
- Repo updated
- First seen
- Licence
- Custom licence
At a glance
This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype.
- Tasks that involve Transcription
- 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
- Tasks that involve Bioinformatics
What it does
Bioconductor Cageminer is an agent skill from bioMate-AI/biomate-bioconductor-kb. This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally, the mined candidates can be given a score that favor candidates that are hubs and/or transcription factors. The scores can then be used to rank and select the top n most promising genes for downstream experiments.
Its SKILL.md is about 1.3k 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 Media & Creative, covering Transcription and Bioinformatics. 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 Transcription
- Tasks that involve Bioinformatics
Example prompts
- “/bioconductor-cageminer”
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 Cageminer loads about 1.3k tokens when it runs. Until then it costs about 124 tokens; SKILL.md has 379 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 379 words (~1,266 tokens).
“Integrate GWAS SNPs and coexpression networks to mine and score high-confidence candidate genes.”
- name
- bioconductor-cageminer
- when_to_use
- Use when: Mining high-confidence candidate genes with cageminer. Not for: Requires R ≥ 4.1 and Bioconductor ≥ 3.16
- user-invocable
- false
Files
Just SKILL.md in skills/transcriptomics/cageminer of bioMate-AI/biomate-bioconductor-kb.
Open the folder on GitHubat commit c9bd4d8
Compare with similar skills
Bioconductor Cageminer 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 Cageminer this skillbioMate-AI/biomate-bioconductor-kb | 804 | — | ~1.3k | Automated safety check: Pass | Custom licence | |
| Bio Motif SearchGPTomics/bioSkills | 1.2k | 1 repos | ~2.9k | Automated safety check: Pass | MIT | |
| Bio Transcription TranslationGPTomics/bioSkills | 1.2k | 1 repos | ~3.4k | Automated safety check: Pass | MIT | |
| Bio Chipseq Super EnhancersGPTomics/bioSkills | 1.2k | 2 repos | ~4.1k | Automated safety check: Pass | MIT | |
| Bio Chipseq Super EnhancersFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~2.1k | Automated safety check: Pass | None | |
| Bio Chipseq Peak CallingFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | — | ~2k | Automated safety check: Pass | None |
Similar skills
Bio Transcription Translation
GPTomics/bioSkills
Transcribe DNA to RNA and translate to protein using Biopython, with NCBI codon-table selection, CDS validation, and six-frame ORF finding.
Bio Chipseq Super Enhancers
GPTomics/bioSkills
Identifies super-enhancers from H3K27ac, MED1, or BRD4 ChIP-seq using ROSE, ROSE2, LILY, HOMER -style super, and ENCODE dELS cross-referencing.
Bio Chipseq Super Enhancers
FreedomIntelligence/OpenClaw-Medical-Skills
Identifies super-enhancers from H3K27ac ChIP-seq data using ROSE and related tools.
Bio Chipseq Peak Calling
FreedomIntelligence/OpenClaw-Medical-Skills
ChIP-seq peak calling using MACS3 (or MACS2). An agent skill from FreedomIntelligence/OpenClaw-Medical-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.
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Implements a variety of methods for batch correction of single-cell (RNA sequencing) data.
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Related
Categories
Questions about Bioconductor Cageminer
What does Bioconductor Cageminer do?
This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. Bioconductor Cageminer is an agent skill from bioMate-AI/biomate-bioconductor-kb. This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype.
When should I use Bioconductor Cageminer?
Bioconductor Cageminer fits situations like: tasks that involve Transcription; tasks that involve Bioinformatics.
How do I install Bioconductor Cageminer in Claude Code?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-cageminer -a claude-code`. Or copy the skill folder (skills/transcriptomics/cageminer in bioMate-AI/biomate-bioconductor-kb) into .claude/skills/bioconductor-cageminer in your project. Claude Code loads it when a task matches its description.
How do I install Bioconductor Cageminer in Codex?
Run `npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-cageminer -a codex`. Or copy the skill folder (skills/transcriptomics/cageminer in bioMate-AI/biomate-bioconductor-kb) into .agents/skills/bioconductor-cageminer in your project. Codex loads it when a task matches its description.
Can I use Bioconductor Cageminer 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-cageminer -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-cageminer, .gemini/skills/bioconductor-cageminer, .github/skills/bioconductor-cageminer and .opencode/skills/bioconductor-cageminer in your project.
What does Bioconductor Cageminer need to run?
SKILL.md names no scripts, command-line tools or credentials: Bioconductor Cageminer is instructions for the agent only.
Does Bioconductor Cageminer 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 Cageminer 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 Cageminer use?
Bioconductor Cageminer 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 Cageminer use?
About 1.3k tokens (SKILL.md is roughly 5.1k 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 Cageminer?
Skills that share tags, products or a category with Bioconductor Cageminer: Bio Motif Search (GPTomics/bioSkills, 1.2k stars), Bio Transcription Translation (GPTomics/bioSkills, 1.2k stars), Bio Chipseq Super Enhancers (GPTomics/bioSkills, 1.2k stars) and Bio Chipseq Super Enhancers (FreedomIntelligence/OpenClaw-Medical-Skills, 3.1k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bioconductor Cageminer?
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.