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lib-scikit-bio

Analyze biological data with sequence manipulation, alignment, and diversity metrics.

Updated Mar 13, 2026
Search Tags:#bioinformatics#genomics#sequence analysis#ecology#phylogenetics#microbiome
One-click install
npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-scikit-bio
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: lib-scikit-bio
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/lib-scikit-bio
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill lib-scikit-bio

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill streamlines complex bioinformatics analyses, from sequence manipulation to microbial ecology, by providing a comprehensive Python toolkit.

Core Features & Use Cases

  • Sequence Analysis: Process DNA, RNA, and protein sequences, including alignment and motif finding.
  • Phylogenetic Tree Construction: Build and analyze evolutionary relationships.
  • Diversity Metrics: Calculate alpha and beta diversity for ecological data.
  • Ordination & Statistics: Perform PCoA, PERMANOVA, and other statistical tests on biological data.
  • Use Case: Analyze microbiome data by reading a BIOM table, calculating beta diversity using UniFrac distances, and visualizing sample relationships with PCoA.

Quick Start

Use the lib-scikit-bio skill to calculate the Shannon diversity for the provided counts matrix.

Frequently Asked Questions about lib-scikit-bio

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

FAQPage Schema
How do I calculate beta diversity and visualize microbiome sample relationships?▼

To calculate beta diversity and visualize microbiome samples, you can read a BIOM table, compute UniFrac distances, and perform PCoA ordination to plot sample relationships.

Can I process DNA, RNA, and protein sequences for alignment and motif finding?▼

Yes, you can process DNA, RNA, and protein sequences for alignment and motif finding, as the toolkit supports comprehensive sequence manipulation and analysis workflows.

How do I calculate Shannon diversity for a biological counts matrix?▼

You can calculate Shannon diversity for a counts matrix by applying the toolkit's alpha diversity metrics functions directly to your ecological data.

What is the best way to perform ordination and statistical testing on biological data?▼

The best way to perform ordination and statistical testing on biological data is by using built-in methods like PCoA for visualization and PERMANOVA for statistical significance testing.

Does this toolkit support building and analyzing phylogenetic trees?▼

Yes, it supports phylogenetic tree construction, allowing you to build and analyze evolutionary relationships directly within your bioinformatics workflow.

What biological file formats are supported for sequence analysis and ecology metrics?▼

It supports various biological file formats, integrating with common bioinformatics workflows to enable sequence analysis and ecological diversity metrics calculations.

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