bioinformatics

Name: bioinformatics
Availability: InStock
Author: thisismynewfmail-ui

Fetch curated bioinformatics skills and pipelines for genomics workflows.

Updated Apr 12, 2026

Search Tags:#skills #bioinformatics #genomics #pipelines #sequencing #variant-calling

Ready to run

npx skills add https://github.com/thisismynewfmail-ui/Monika-agent --skill bioinformatics-thisismynewfmail-ui

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: bioinformatics
Source: https://github.com/thisismynewfmail-ui/Monika-agent/tree/main/optional-skills/research/bioinformatics
Command: npx skills add https://github.com/thisismynewfmail-ui/Monika-agent --skill bioinformatics-thisismynewfmail-ui

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Provides a single gateway to discover and fetch hundreds of domain-specific bioinformatics skills and runnable pipelines so users need not bundle or memorize many separate repos and formats.

Core Features & Use Cases

Indexed Reference Library: Indexes bioSkills (385 reference topics) and ClawBio (33 runnable pipelines) and points to the exact SKILL.md, README, or pipeline bundle for each task.
On-Demand Fetching: Guides shallow cloning and selective retrieval of skill pages or pipeline directories when a topic is requested, minimizing disk use.
Practical Use Cases: Quickly find recommended parameter sets for variant calling, runnable demo pipelines for RNA-seq differential expression, Scanpy/Seurat single-cell workflows, or reproducible metagenomics pipelines with environment files.

Quick Start

Clone the referenced repositories with shallow clones and request a specific topic such as "variant-calling gatk-variant-calling" to fetch the corresponding SKILL.md and pipeline artifacts.

Frequently Asked Questions about bioinformatics

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

FAQPage Schema

How do I find runnable genomics pipelines for tasks like RNA-seq differential expression or variant calling?▼

You can discover genomics pipelines by requesting topics like variant calling or RNA-seq differential expression to fetch curated SKILL.md files and pipeline bundles from indexed bioSkills and ClawBio repositories on demand.

Do I need conda and samtools installed before running bioinformatics workflows?▼

Yes, you typically need conda, samtools, bcftools, and common Python or R libraries installed in your environment, as the fetched bioinformatics pipelines and skills provide guidance on required tools but do not bundle the executables themselves.

Can I use this to access single-cell analysis workflows with Scanpy or Seurat?▼

Yes, you can access single-cell analysis workflows with Scanpy or Seurat by requesting the relevant topic to retrieve reproducible pipeline directories and environment files from the indexed reference library of bioinformatics skills.

What is the best way to retrieve metagenomics pipelines without using excessive disk space?▼

The best way to retrieve metagenomics pipelines without excessive disk use is through guided shallow cloning, which selectively fetches only the requested skill pages or pipeline directories from the indexed repositories.

Does this bioinformatics skill bundle all sequencing and structural biology tools into one download?▼

No, it does not bundle tools into one download. It acts as a gateway to discover and selectively fetch hundreds of domain-specific skills and runnable pipelines for sequencing and structural biology, minimizing disk use through shallow cloning.

How do I get recommended parameter sets for GATK variant calling?▼

To get recommended parameter sets for GATK variant calling, request the variant-calling topic to fetch the corresponding SKILL.md and pipeline artifacts, which provide practical parameter configurations and workflow guidance.