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Bioskills

skill-gptomics-bioskills-bioskills-installer · by GPTomics

Installs 425 bioinformatics skills covering sequence analysis, RNA-seq, single-cell, variant calling, metagenomics, structural biology, and 56 more categories. Use when setting up bioinformatics capabilities or when a bioinformatics task requires specialized skills not yet installed.

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Install

$ agentstack add skill-gptomics-bioskills-bioskills-installer

✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.

Security review

✓ Passed

No issues found. Passed automated security review. · v0.1.0 How review works →

  • ✓ Prompt-injection patterns
  • ✓ Secret / credential exfiltration
  • ✓ Dangerous shell & filesystem operations
  • ✓ Untrusted network calls
  • ✓ Known-malicious package signatures

What it can access

  • ✓ Network access No
  • ✓ Filesystem access No
  • ✓ Shell / process execution No
  • ✓ Environment & secrets No
  • ✓ Dynamic code execution No

From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.

View the full security report →

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Reliability & compatibility

✓ Security review passed
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● 1mo ago

Declared compatibility

Claude CodeClaude Desktop

Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.

Preview Execution monitoring

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About

bioSkills Installer

Meta-skill that installs the full bioSkills collection (425 skills across 62 categories) for bioinformatics analysis.

Installation

Run the bundled install script to download and install all bioSkills:

bash scripts/install-bioskills.sh

Or install only specific categories:

bash scripts/install-bioskills.sh --categories "single-cell,variant-calling,differential-expression"

What Gets Installed

425 skills across 62 categories covering:

  • Sequence & Alignment (40): sequence-io, sequence-manipulation, alignment, alignment-files, database-access
  • Read Processing (11): read-qc, read-alignment
  • RNA-seq & Expression (14): differential-expression, rna-quantification, expression-matrix
  • Single-Cell & Spatial (25): single-cell, spatial-transcriptomics
  • Variant Analysis (21): variant-calling, copy-number, phasing-imputation
  • Epigenomics (25): chip-seq, atac-seq, methylation-analysis, hi-c-analysis
  • Metagenomics & Microbiome (13): metagenomics, microbiome
  • Genomics & Assembly (29): genome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design
  • Regulatory & Causal (13): gene-regulatory-networks, causal-genomics, rna-structure
  • Temporal & Ecological (11): temporal-genomics, ecological-genomics
  • Immunology & Clinical (25): immunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics
  • Specialized Omics (36): proteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy
  • RNA Biology (20): small-rna-seq, epitranscriptomics, clip-seq, ribo-seq
  • Phylogenetics & Evolution (16): phylogenetics, population-genetics, comparative-genomics
  • Structural & Systems (11): structural-biology, systems-biology
  • Screens & Cytometry (22): crispr-screens, flow-cytometry, imaging-mass-cytometry
  • Pathway & Integration (14): pathway-analysis, multi-omics-integration, restriction-analysis
  • Infrastructure (39): data-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing
  • Workflows (40): end-to-end pipelines (FASTQ to results)

After Installation

Once installed, skills are automatically triggered based on the task at hand. Example requests:

  • "I have RNA-seq counts from treated vs control samples - find the differentially expressed genes"
  • "Call variants from this whole genome sequencing BAM file"
  • "Cluster my single-cell RNA-seq data and find marker genes"
  • "Predict the structure of this protein sequence"
  • "Run a metagenomics classification on these shotgun reads"

Source

GitHub: https://github.com/GPTomics/bioSkills

Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

Install and usage instructions live in the source repository linked above.

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Versions

  • v0.1.0 Imported from the upstream source.

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