Does scikit-bio support protein language models?

Yes, it includes capabilities for working with protein embeddings from models like ESM and ProtTrans to facilitate downstream analysis and visualization.

What biological file formats does the scikit-bio skill support?

It supports over 19 biological formats including FASTA, FASTQ, GenBank, Newick, BIOM, and Clustal, often featuring automatic format detection.

How does the skill handle large genomic datasets?

The skill utilizes memory-efficient generators for file I/O and implements scalable algorithms for tree construction to handle large-scale biological data.

Can I use this skill for microbiome research?

Yes, it is specifically designed for microbiome analysis, including diversity metrics (Alpha/Beta), UniFrac distances, and statistical tests like PERMANOVA.

Scikit-bio Bioinformatics Toolkit

Name: Scikit-bio Bioinformatics Toolkit
Author: pur3v4d3r

bypur3v4d3r

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Data Science & ML

Performs comprehensive biological data analysis, including sequence manipulation, phylogenetics, and microbiome ecology statistics.

About

Scikit-bio is a specialized Claude Code skill that empowers researchers and developers to conduct sophisticated bioinformatics workflows directly within their coding environment. It provides robust tools for handling biological sequences (DNA, RNA, protein), constructing and analyzing phylogenetic trees, and calculating complex ecological diversity metrics like UniFrac. Whether you are performing multivariate statistics (PCoA, PERMANOVA), managing BIOM tables, or integrating protein embeddings from modern language models, this skill provides the domain-specific logic and implementation patterns necessary for rigorous scientific discovery.

Key Features

Advanced phylogenetic tree construction and manipulation including NJ and UPGMA.
Microbiome diversity analysis featuring Alpha/Beta metrics and UniFrac distances.
Multivariate statistical testing and ordination methods like PCoA, CCA, and PERMANOVA.
Extensive support for 19+ biological file formats including FASTA, FASTQ, and BIOM.
Comprehensive sequence manipulation for DNA, RNA, and protein data with validation.
1 GitHub stars

Use Cases

Analyzing microbial community structures and calculating community diversity metrics.
Performing sequence alignments and searching for motifs in genomic or proteomic data.
Automating bioinformatics pipelines for sequence format conversion and data cleaning.

About

Key Features

Advanced phylogenetic tree construction and manipulation including NJ and UPGMA.
Microbiome diversity analysis featuring Alpha/Beta metrics and UniFrac distances.
Multivariate statistical testing and ordination methods like PCoA, CCA, and PERMANOVA.
Extensive support for 19+ biological file formats including FASTA, FASTQ, and BIOM.
Comprehensive sequence manipulation for DNA, RNA, and protein data with validation.
1 GitHub stars

Use Cases

Analyzing microbial community structures and calculating community diversity metrics.
Performing sequence alignments and searching for motifs in genomic or proteomic data.
Automating bioinformatics pipelines for sequence format conversion and data cleaning.