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JamesFincher
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bioinformatics

Retrieve domain-indexed bioinformatics guidance for genomics and computational biology workflows.

Updated May 4, 2026
Search Tags:#bioinformatics#genomics#single-cell#pipelines#RNA-seq#reference materials#variant calling
One-click install
npx skills add https://github.com/JamesFincher/gengar --skill bioinformatics-jamesfincher
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioinformatics
Source: https://github.com/JamesFincher/gengar/tree/main/optional-skills/research/bioinformatics
Command: npx skills add https://github.com/JamesFincher/gengar --skill bioinformatics-jamesfincher

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

The bioinformatics skill helps you quickly find credible reference guidance and runnable analysis workflows for complex genomics and computational biology tasks without manually researching parameters across many sources.

Core Features & Use Cases

  • Domain-indexed bioinformatics access: Gatekeeps hundreds of topic-specific skills covering genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, and more.
  • On-demand reference and runnable pipelines: Retrieves reference material from bioSkills (code patterns, decision trees, parameter guides) and pipeline-style runnable skills from ClawBio (Python scripts and reproducibility bundles).
  • Practical workflow selection: Helps you choose the right skill from an indexed domain map for tasks like read QC, alignment, VCF annotation, differential expression, and pathway enrichment.

Quick Start

Tell Gengar to fetch the best matching bioinformatics skill for your task, e.g., "bioinformatics: I need a reference guide for variant calling and filtering best practices for whole-genome sequencing VCFs."

Frequently Asked Questions about bioinformatics

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

FAQPage Schema
How do I find reference workflows for RNA-seq and single-cell analysis?▼

You can retrieve expert bioinformatics guidance for RNA-seq and single-cell workflows by requesting domain-indexed reference materials and runnable pipelines. The skill fetches decision trees, code patterns, and Python scripts from cloned bioSkills and ClawBio repositories.

What is the best way to structure variant calling and VCF annotation pipelines?▼

Variant calling and VCF annotation workflows are organized as topic-specific skills within a domain map. The skill retrieves parameter guides and reproducibility bundles on demand, helping you select the appropriate runnable pipeline for whole-genome sequencing tasks.

Do I need to clone repositories before fetching genomics pipelines?▼

Yes, fetching genomics pipelines requires cloning the GPTomics/bioSkills and ClawBio repositories. This setup provides the skill with access to reference materials and runnable scripts needed to retrieve expert bioinformatics guidance.

Can I use this for metagenomics and structural biology questions?▼

Metagenomics and structural biology questions are fully supported. The skill organizes hundreds of topic-specific skills across computational biology domains, allowing you to retrieve relevant reference guides and workflows on demand.

How do I get read QC and alignment best practices?▼

Read QC and alignment best practices are retrieved by asking the skill to fetch the matching bioinformatics skill for your task. It provides indexed reference material including code patterns, parameter guides, and decision trees.

Are the bioinformatics workflows runnable or just reference guides?▼

The workflows include both reference guides and runnable pipelines. Reference materials come from bioSkills, offering code patterns and decision trees, while ClawBio provides pipeline-style runnable skills containing Python scripts and reproducibility bundles.

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