Bioconductor Bridge

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

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

# 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

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

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

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

• Bioconductor — official project and package ecosystem
• BiocManager — official installation and version-management guidance
• SummarizedExperiment — canonical assay container
• SingleCellExperiment — canonical single-cell container
• GenomicRanges — canonical interval container
• VariantAnnotation — canonical VCF and variant annotation package