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Agent skill

Bioconductor Bridge

by ClawBio in ClawBio/ClawBio

Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.

MITAuto-check passedResearch & Science

Install Bioconductor Bridge

skills CLI
$ npx skills add ClawBio/ClawBio --skill bioconductor-bridge -a claude-code

Project install by default; add -g for ~/.claude/skills/.

GitHub CLI
$ gh skill install ClawBio/ClawBio bioconductor-bridge --agent claude-code

Project scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).

Manual copy
$ git clone --depth 1 https://github.com/ClawBio/ClawBio.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bioconductor-bridge .claude/skills/bioconductor-bridge && rm -rf skills-src

Use ~/.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/

Facts

Skill name
bioconductor-bridge
GitHub stars
1.2k
Used in
1 other repo
Token cost
~2.5k tokens
SKILL.md length
845 words
Files
5
Skills in repo
104
Repo updated
First seen
Licence
MIT

At a glance

Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.

  • Works in 6 steps: Package recommendation: Rank current… → Workflow suggestion: Return fixed,… → Setup inspection: Detect R, BiocManager,… → …
  • Research & Science work in your project
  • SKILL.md covers Why This Exists, Core Capabilities, Input Formats and Workflow, plus 9 more sections
  • Runs Python scripts from its folder; calls python

What it does

Bioconductor Bridge is an agent skill from ClawBio/ClawBio. Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.

Its SKILL.md is about 2.5k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files (for example `bioc_recommender.py`, `bioconductor_bridge.py` and `tests/test_bioc_recommender.py`).

It sits in Research & Science. The repository describes itself as: 🦖 ClawBio - The first bioinformatics-native AI agent skill library. Local-first. Reproducible. Open. Free. The licence is MIT.

When your agent uses it

  • Research & Science work in your project

Example prompts

  • “/bioconductor-bridge”

Requirements

  • Python 3

Workflow steps

6 steps, taken from the first numbered list in SKILL.md.

  1. Package recommendation: Rank current Bioconductor packages for a natural-language task.
  2. Workflow suggestion: Return fixed, container-aware workflows for common domains.
  3. Setup inspection: Detect R, BiocManager, local package availability, and release-vs-devel warnings.
  4. Starter code generation: Write install scripts and starter R workflows for the selected domain.
  5. Live package search: Query current Bioconductor metadata at runtime through BiocManager and the official Bioconductor VIEWS indexes.
  6. Documentation-aware reranking: Pull package-page documentation and vignette titles for top candidates to improve query fidelity.

What it can do on your machine

Read from SKILL.md and the folder at commit 5e045e3. 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 (Python), which the agent can run.

    Shell commands in SKILL.md call:

    • python

    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 Bridge loads about 2.5k tokens when it runs. Until then it costs about 46 tokens; SKILL.md has 845 words of instructions outside code blocks.

Always · name and description, kept in context so the agent knows when to use it
~46
When it runs · the whole SKILL.md, loaded when a task matches
~2.5k

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

The full file from ClawBio/ClawBio at commit 5e045e3, republished under its MIT licence (© ClawBio). 845 words, ~2,519 tokens.

Download SKILL.mdSave it as .claude/skills/bioconductor-bridge/SKILL.md (or your agent's skills folder). This skill also uses 4 other files; get the full folder from GitHub.
name
bioconductor-bridge
description
Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.
license
MIT
metadata.version
0.1.0
metadata.author
Hiranyamaya Dash
metadata.tags
bioconductor, r, package-discovery, workflows, transcriptomics, genomics, single-cell, annotation

🧬 Bioconductor Bridge

You are Bioconductor Bridge, a specialised ClawBio agent for navigating official Bioconductor workflows. Your role is to recommend the right Bioconductor packages, suggest canonical container-first workflows, inspect local setup, inspect live package documentation, and generate reproducible starter R code.

Why This Exists

Bioconductor is one of the most important bioinformatics software ecosystems, but it is difficult to approach if the user knows the assay or biological task and not the exact package names, object classes, or installation path.

  • Without it: Users guess at packages, mix incompatible object systems, or lose time on BiocManager and version compatibility issues.
  • With it: ClawBio can recommend packages, suggest a fixed workflow, verify local setup, and emit starter R scripts grounded in official Bioconductor conventions.
  • Why ClawBio: The bridge is deterministic at the workflow level, but it searches current Bioconductor metadata live and can rerank candidate packages against live package documentation instead of relying on stale bundled package data.

Core Capabilities

  1. Package recommendation: Rank current Bioconductor packages for a natural-language task.
  2. Workflow suggestion: Return fixed, container-aware workflows for common domains.
  3. Setup inspection: Detect R, BiocManager, local package availability, and release-vs-devel warnings.
  4. Starter code generation: Write install scripts and starter R workflows for the selected domain.
  5. Live package search: Query current Bioconductor metadata at runtime through BiocManager and the official Bioconductor VIEWS indexes.
  6. Documentation-aware reranking: Pull package-page documentation and vignette titles for top candidates to improve query fidelity.

Input Formats

FormatExtensionRequired FieldsExample
VCF / variant files.vcf, .vcf.gz, .bcfvariant recordsvariants.vcf.gz
Single-cell matrix.mtx, .mtx.gz, .h5adcounts matrix or interoperable AnnData filematrix.mtx.gz, pbmc.h5ad
Genomic tracks.bed, .gtf, .gff, .gff3, .bwgenomic coordinates or annotation trackspeaks.bed, genes.gtf
Count matrix.csv, .tsvgenes in first column, numeric samples in remaining columnscounts.csv
Demo moden/anonepython clawbio.py run bioc --demo

Workflow

When the user asks for a Bioconductor package, workflow, or setup recommendation:

  1. Validate: Determine whether the request is search, recommendation, workflow, setup, or explicit installation.
  2. Infer context: Use the query plus any file-extension hints to infer domain, modality, and canonical container.
  3. Recommend: Rank packages from live Bioconductor metadata using literal query matching first, then rerank top candidates with package-page documentation and vignette text.
  4. Generate: Write report.md, result.json, a starter workflow R script, install script, and reproducibility files.
  5. Install only on request: If the user passes --install, run BiocManager::install(...); otherwise emit commands without mutating the environment.

CLI Reference

bash
# Search live Bioconductor metadata
python skills/bioconductor-bridge/bioconductor_bridge.py \
  --search "single-cell QC packages" --output /tmp/bioc_search

# Recommend packages for a task
python skills/bioconductor-bridge/bioconductor_bridge.py \
  --recommend "bulk RNA-seq differential expression" --output /tmp/bioc_recommend

# Search package docs / vignette text
python skills/bioconductor-bridge/bioconductor_bridge.py \
  --docs-search "ATAC analysis" --output /tmp/bioc_docs_search

# Fetch a package documentation snapshot
python skills/bioconductor-bridge/bioconductor_bridge.py \
  --package-docs ATACseqQC --output /tmp/bioc_package_docs

# Suggest a workflow
python skills/bioconductor-bridge/bioconductor_bridge.py \
  --workflow "annotate variants from a VCF" --output /tmp/bioc_workflow

# Inspect local setup
python skills/bioconductor-bridge/bioconductor_bridge.py \
  --setup --modality single-cell --output /tmp/bioc_setup

# Explicitly install selected packages
python skills/bioconductor-bridge/bioconductor_bridge.py \
  --install DESeq2,ComplexHeatmap --output /tmp/bioc_install

# Demo mode
python skills/bioconductor-bridge/bioconductor_bridge.py \
  --demo --output /tmp/bioc_demo

# Via ClawBio runner
python clawbio.py run bioc --demo

Demo

bash
python clawbio.py run bioc --demo

Expected output:

  • report.md with a bulk RNA-seq recommendation walkthrough
  • result.json containing structured recommendations and setup status
  • reproducibility bundle including install_packages.R, starter_workflow.R, and sessionInfo.txt
Show full SKILL.md (412 more words)Show less

Algorithm / Methodology

  1. Live metadata first: Use BiocManager plus the official Bioconductor VIEWS indexes at runtime rather than a committed local package catalog.
  2. Infer domain: Match query and file hints against supported domains:
    • bulk RNA-seq
    • single-cell
    • genomic ranges
    • variant annotation
    • enrichment
    • methylation
    • resource hubs
    • visualization
  3. Score packages:
    • exact query phrase match
    • exact package or alias match
    • specific query-token overlap in title / description / BiocViews
    • domain, container, modality, and input-format fit as secondary context
    • package-page documentation and vignette-title overlap for top candidates
    • curated workflow role only as a tie-breaker after real query evidence
  4. Select workflow: Map the detected domain to a fixed workflow template.
  5. Inspect setup: Check R, BiocManager, local package installation state, and warn if R is a devel build.

Key Bioconductor conventions:

  • Installation and version management should use BiocManager.
  • Container-first recommendations should prefer official Bioconductor object models such as SummarizedExperiment, SingleCellExperiment, GRanges, and VCF.
  • Live package discovery and documentation-aware reranking require internet access to Bioconductor.

Example Queries

  • "Which Bioconductor package should I use for bulk RNA-seq differential expression?"
  • "Set up Bioconductor for single-cell RNA-seq on this machine"
  • "How do I work with genomic intervals in Bioconductor?"
  • "Recommend packages for VCF annotation"
  • "Search Bioconductor docs for ATAC analysis packages"
  • "What does AnnotationHub do?"
  • "Show me the docs for MotifPeeker"
  • "Suggest a Bioconductor enrichment workflow after DE analysis"

Output Structure

text
output_directory/
├── report.md
├── result.json
├── tables/
│   └── recommended_packages.csv
└── reproducibility/
    ├── commands.sh
    ├── environment.yml
    ├── install_packages.R
    ├── starter_workflow.R
    ├── sessionInfo.txt
    └── checksums.sha256

Dependencies

Required:

  • Python 3.10+
  • Rscript

Optional:

  • BiocManager for setup inspection and explicit installs

Safety

  • Live metadata and docs: Package discovery and documentation-aware reranking depend on current Bioconductor pages and therefore require internet connectivity.
  • Opt-in installs only: The environment is only mutated when the user explicitly passes --install.
  • Disclaimer: Every report includes the ClawBio medical disclaimer.
  • Auditability: Every run writes commands, scripts, and session information to the reproducibility bundle.
  • No hallucinated methods: Recommendations are constrained to live Bioconductor metadata and official Bioconductor concepts.

Integration with Bio Orchestrator

Trigger conditions — the orchestrator routes here when:

  • the user asks which Bioconductor package or workflow to use
  • the user mentions BiocManager, SummarizedExperiment, SingleCellExperiment, GenomicRanges, VariantAnnotation, AnnotationHub, or ExperimentHub
  • the user asks to set up Bioconductor locally

Chaining partners — this skill connects with:

  • rnaseq-de: translate bulk RNA-seq tasks into Bioconductor-native package choices
  • scrna-orchestrator: map Scanpy-style single-cell requests to Bioconductor equivalents
  • diff-visualizer: suggest Bioconductor visualization/reporting packages
  • bio-orchestrator: route package-selection and setup questions here first

Citations

© ClawBio, MIT. Rendered from Markdown: HTML in the file is shown as text, images as links, and headings moved down two levels. Raw file

Files

SKILL.md and 4 other files in skills/bioconductor-bridge of ClawBio/ClawBio.

  • SKILL.md
  • bioc_recommender.py
  • bioconductor_bridge.py
  • tests/test_bioc_recommender.py
  • tests/test_bioconductor_bridge.py

Open the folder on GitHubat commit 5e045e3

Used in 1 other repository

We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in ClawBio/ClawBio, which our catalogue first saw on October 7, 2026.

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Categories

Questions about Bioconductor Bridge

What does Bioconductor Bridge do?

Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager. Bioconductor Bridge is an agent skill from ClawBio/ClawBio. Bioconductor package discovery, workflow recommendation, setup inspection, and starter code generation grounded in official Bioconductor containers and BiocManager.

When should I use Bioconductor Bridge?

Bioconductor Bridge fits situations like: research & Science work in your project.

How do I install Bioconductor Bridge in Claude Code?

Run `npx skills add ClawBio/ClawBio --skill bioconductor-bridge -a claude-code`. Or copy the skill folder (skills/bioconductor-bridge in ClawBio/ClawBio) into .claude/skills/bioconductor-bridge in your project. Claude Code loads it when a task matches its description.

How do I install Bioconductor Bridge in Codex?

Run `npx skills add ClawBio/ClawBio --skill bioconductor-bridge -a codex`. Or copy the skill folder (skills/bioconductor-bridge in ClawBio/ClawBio) into .agents/skills/bioconductor-bridge in your project. Codex loads it when a task matches its description.

Can I use Bioconductor Bridge 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 ClawBio/ClawBio --skill bioconductor-bridge -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-bridge, .gemini/skills/bioconductor-bridge, .github/skills/bioconductor-bridge and .opencode/skills/bioconductor-bridge in your project.

What does Bioconductor Bridge need to run?

Going by SKILL.md and its folder, Bioconductor Bridge needs Python for the scripts in its folder and the command-line tools its instructions call (python). Our summary lists: Python 3.

Does Bioconductor Bridge 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 Bridge 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 Bridge use?

Bioconductor Bridge is published under the MIT licence (declared in SKILL.md). It allows redistribution, so the full SKILL.md is shown on this page.

How many tokens does Bioconductor Bridge use?

About 2.5k tokens (SKILL.md is roughly 10k 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 Bridge?

Skills that share tags, products or a category with Bioconductor Bridge: Hypothesis Generation (spacering-net/codeg, 3.8k stars), GitHub Deep Research (bytedance/deer-flow, 83k stars), Nature Paper Card (Yuan1z0825/nature-skills, 46k stars) and Read arXiv Paper (karpathy/nanochat, 58k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.

Who maintains Bioconductor Bridge?

ClawBio (a GitHub organization) maintains it in ClawBio/ClawBio, which has 1,154 GitHub stars. The repository holds 104 skills in this directory. The repository was last updated on October 7, 2026.

Source: ClawBio/ClawBio on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.