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Chensihakniroth
ChensihaknirothCOMMUNITY
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bioinformatics

Indexes and fetches 400+ bioinformatics reference skills and runnable pipelines from bioSkills and ClawBio repositories.

Updated Jun 7, 2026
Search Tags:#bioinformatics#genomics#single-cell#pipelines#RNA-seq#metagenomics#variant calling
One-click install
npx skills add https://github.com/Chensihakniroth/ANAKOT-AGENT --skill bioinformatics-chensihakniroth
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: bioinformatics
Source: https://github.com/Chensihakniroth/ANAKOT-AGENT/tree/main/optional-skills/research/bioinformatics
Command: npx skills add https://github.com/Chensihakniroth/ANAKOT-AGENT --skill bioinformatics-chensihakniroth

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Bioinformatics work spans hundreds of specialized domains, and no single skill can bundle correct parameters, tool flags, and validated pipelines for all of them. This gateway indexes two open-source skill libraries and fetches the exact domain guide you need on demand. ## Core Features & Use Cases - Domain Skill Index: Covers genomics, transcriptomics, single-cell, variant calling, pharmacogenomics, metagenomics, structural biology, proteomics, CRISPR, and more. - Two Source Libraries: bioSkills provides 385 reference guides with code patterns and parameter best practices; ClawBio provides 33 executable Python pipelines with demo flags and reproducibility bundles. - Use Case: When asked to annotate a VCF file, clone the ClawBio repo, read the vcf-annotator skill, and follow its VEP + ClinVar + gnomAD pipeline with validated parameters. ## Quick Start Ask the agent to fetch the appropriate bioinformatics skill for your task, for example: run a differential expression analysis on my RNA-seq count matrix using the rnaseq-de pipeline.

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 this skill?▼

Identify the variant-calling domain in the index, shallow clone the relevant repo, and read the specific skill such as gatk-variant-calling from bioSkills or vcf-annotator from ClawBio. Follow the fetched guide for correct tool flags and parameters.

What is the difference between bioSkills and ClawBio?▼

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

Does this skill work on Windows?▼

The skill metadata lists linux and macos as supported platforms. Most underlying bioinformatics CLI tools like samtools and bcftools are also primarily distributed for Linux and macOS, often via Conda or package managers.

What dependencies are required for bioinformatics pipelines?▼

Common dependencies include Python packages like biopython, pysam, scanpy, and anndata, R/Bioconductor packages like DESeq2 and edgeR, and CLI tools like samtools, bcftools, and minimap2. Conda with the bioconda channel is recommended for reproducibility.

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 agent skills.

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