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bioinformatics

Indexes and fetches genomics and computational biology skills from two open-source repositories.

Updated Sep 10, 2026
Search Tags:#bioinformatics#genomics#single-cell#RNA-seq#pharmacogenomics#metagenomics#variant calling
One-click install
npx skills add https://github.com/loteiron/ZeusAgent --skill bioinformatics-loteiron
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioinformatics
Source: https://github.com/loteiron/ZeusAgent/tree/main/optional-skills/research/bioinformatics
Command: npx skills add https://github.com/loteiron/ZeusAgent --skill bioinformatics-loteiron

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Bioinformatics work spans hundreds of specialized domains, and no single skill can cover them all. This gateway indexes 400+ genomics and computational biology skills from two open-source libraries and fetches the exact reference guide or runnable pipeline you need on demand. ## Core Features & Use Cases - Domain Skill Index: Browse an organized catalog covering variant calling, RNA-seq, single-cell analysis, metagenomics, pharmacogenomics, structural biology, and more. - Two Complementary Sources: Access bioSkills (385 reference guides with code patterns and parameter best practices) and ClawBio (33 executable pipelines with reproducibility bundles). - On-Demand Fetching: Shallow-clone the relevant repository and read only the specific skill needed, avoiding bloat. - 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 agent to help with a bioinformatics task such as running a differential expression analysis on RNA-seq count data, and it will fetch the appropriate domain skill.

Frequently Asked Questions about bioinformatics

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

FAQPage Schema
How do I find the right bioinformatics skill for my analysis?▼

Identify your domain in the skill index, which is organized by areas like variant calling, RNA-seq, single-cell, and metagenomics. Then shallow-clone the relevant repository and read the specific skill file at the listed path.

What is the difference between bioSkills and ClawBio?▼

bioSkills provides 385 reference guides with code patterns, parameter recommendations, and decision trees. ClawBio provides 33 executable Python pipelines, many with demo flags, that export reports, command logs, and environment files.

Can I run ClawBio pipelines directly after cloning?▼

Yes, many ClawBio skills are executable and include --demo flags. First run pip install -r requirements.txt in the cloned repository, and ensure required bioinformatics tools like samtools or bcftools are installed.

What tools do I need installed for bioinformatics analysis?▼

Common dependencies include Python packages like biopython, pysam, and scanpy, R/Bioconductor packages like DESeq2 and edgeR, and CLI tools like samtools, bcftools, and bedtools. Conda with the bioconda channel is recommended for reproducibility.

Are the fetched skills in ZeusAgent SKILL.md format?▼

No, the fetched skills use their own structures and should be treated as expert reference material. bioSkills entries are code pattern cookbooks, while ClawBio entries combine READMEs with runnable Python scripts.

What are the limitations of this bioinformatics gateway?▼

The gateway only indexes external repositories, so it requires network access to clone them. Genomic data files can be very large, and pipelines assume prerequisite tools are installed on a Linux or macOS workstation.

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