Does it support protein embeddings from AI models?

Yes, it can work with protein language model embeddings (such as ESM or ProtTrans) and convert them into distance matrices or ordination objects.

What biological file formats does this skill support?

The scikit-bio skill supports over 19 biological formats, including FASTA, FASTQ, GenBank, Newick, BIOM (HDF5 and JSON), and Clustal.

Can I perform statistical testing with scikit-bio?

Yes, it includes specialized non-parametric tests for biological data, such as PERMANOVA, ANOSIM, PERMDISP, and the Mantel test.

Can this skill help with microbiome research?

Yes, it is specifically optimized for microbiome analysis, offering alpha/beta diversity metrics, rarefaction, and ordination methods like PCoA.

Scikit-Bio

Name: Scikit-Bio
Author: ricable

byricable

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データサイエンスとML

Analyzes biological data including sequences, phylogenetic trees, and microbial diversity metrics using specialized Python tools.

概要

Scikit-bio is a comprehensive toolkit for bioinformatics that empowers Claude to perform advanced biological data analysis. It provides specialized capabilities for sequence manipulation, phylogenetic tree construction, and ecological diversity measurements, making it essential for microbiome research, community ecology, and evolutionary biology workflows. Whether calculating UniFrac distances, running PERMANOVA tests, or managing BIOM tables, this skill streamlines the process of extracting scientific insights from complex biological datasets through automated implementation patterns and best practices.

主な機能

Alpha and beta diversity metrics including Faith's PD and UniFrac
Phylogenetic tree construction and analysis using neighbor-joining and UPGMA
1 GitHub stars
Robust support for 19+ biological file formats including FASTA, BIOM, and Newick
Sequence manipulation for DNA, RNA, and protein data with quality score handling
Multivariate ordination methods like PCoA, CCA, and RDA for data visualization

ユースケース

Evolutionary relationship modeling through phylogenetic tree construction
Microbiome community ecology analysis and diversity profiling
High-dimensional biological data reduction and statistical hypothesis testing

概要

主な機能

Alpha and beta diversity metrics including Faith's PD and UniFrac
Phylogenetic tree construction and analysis using neighbor-joining and UPGMA
1 GitHub stars
Robust support for 19+ biological file formats including FASTA, BIOM, and Newick
Sequence manipulation for DNA, RNA, and protein data with quality score handling
Multivariate ordination methods like PCoA, CCA, and RDA for data visualization

ユースケース

Evolutionary relationship modeling through phylogenetic tree construction
Microbiome community ecology analysis and diversity profiling
High-dimensional biological data reduction and statistical hypothesis testing