bioinformatics

Indexes and fetches 400+ bioinformatics skills from bioSkills and ClawBio repositories on demand.

Updated May 3, 2026
One-click install
npx skills add https://github.com/80portisfound/vibe-learning --skill bioinformatics-80portisfound
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioinformatics
Source: https://github.com/80portisfound/vibe-learning/tree/main/packages/hermes/optional-skills/research/bioinformatics
Command: npx skills add https://github.com/80portisfound/vibe-learning --skill bioinformatics-80portisfound

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Bioinformatics spans hundreds of specialized domains, and no single skill can cover them all. This gateway indexes over 400 domain-specific skills from two open-source libraries and fetches the exact reference material or runnable pipeline you need, instead of bundling everything locally. ## Core Features & Use Cases - Domain Index: Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, proteomics, CRISPR, and more, organized by domain. - Two Source Libraries: bioSkills provides 385 reference guides with code patterns and parameter best practices; ClawBio provides 33 executable pipelines with demo flags and reproducibility bundles. - On-Demand Fetching: Shallow-clones the relevant GitHub repo and reads the specific skill file, keeping local footprint minimal. - Use Case: When asked to annotate a VCF file, fetch the ClawBio vcf-annotator pipeline or the bioSkills variant-annotation guide to get correct VEP, ClinVar, and gnomAD parameters. ## Quick Start Ask the assistant to fetch the appropriate bioinformatics skill for your task, for example: fetch the GATK variant calling guide from bioSkills and walk me through the workflow.

Frequently Asked Questions about bioinformatics

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I run a variant calling pipeline with GATK?▼

Fetch the gatk-variant-calling skill from the bioSkills variant-calling category by shallow-cloning the repo and reading its SKILL.md. It provides correct GATK parameters, filtering best practices, and joint-calling guidance as reference material.

What is the difference between bioSkills and ClawBio?▼

bioSkills contains 385 reference guides with code patterns and parameter recommendations that are not directly executable. ClawBio contains 33 runnable Python pipelines, many with --demo flags, that export report.md, commands.sh, and environment.yml.

Can I analyze single-cell RNA-seq data with this skill?▼

Yes. The index covers single-cell preprocessing, clustering, batch integration, and annotation via bioSkills, plus executable ClawBio pipelines like scrna-orchestrator (Scanpy) and scrna-embedding (scVI) for full analysis workflows.

Does this skill work on Windows?▼

No. The skill metadata specifies linux and macos platforms only. Most underlying bioinformatics tools such as samtools, bcftools, and BWA are also primarily distributed for Unix-like systems.

Why do fetched skills not follow the standard SKILL.md format?▼

The fetched skills come from external repositories with their own structures: bioSkills uses code-pattern cookbooks and ClawBio uses README plus Python scripts. Treat them as expert domain reference material rather than native skills.

What are the limitations of this bioinformatics gateway?▼

It requires network access to clone the source repositories and assumes a bioinformatics workstation with tools installed. Genomic data files can be very large, so disk space is a practical constraint when downloading references or SRA datasets.