Compute distances, diversity metrics, and ordinations from biological sequences and trees.
npx skills add https://github.com/CRAG666/dotfiles --skill scikit-bio-crag666
Please help me install this Agent Skill. Skill: scikit-bio Source: https://github.com/CRAG666/dotfiles/tree/main/skills/scikit-bio Command: npx skills add https://github.com/CRAG666/dotfiles --skill scikit-bio-crag666
scikit-bio helps you perform end-to-end bioinformatics and microbial ecology analysis—turning biological sequence, alignment, tree, and count-table data into distances, diversity metrics, ordinations, and statistical test outputs.
Use the scikit-bio skill to compute alpha and beta diversity from a BIOM count table and an input phylogenetic tree, then summarize results with PCoA and run PERMANOVA for group differences.
High-intent search queries and answers about installing and using this skill.
To calculate UniFrac beta diversity, load a BIOM-style feature table and a Newick phylogenetic tree, then run the diversity functions to compute biologically meaningful distance matrices between microbial communities.
Yes, you can run PERMANOVA and Mantel tests on distance matrices to perform distance-based hypothesis testing and determine if microbial community differences between groups are statistically significant.
Reading FASTA and GenBank files uses validated I/O operations to parse biological sequence data, enabling downstream operations like reverse-complement, transcription, translation, and motif regex search.
Computing PCoA ordination axes from distance matrices transforms microbial community distances into principal coordinate axes, allowing you to visualize beta diversity patterns across biological samples.
Yes, phylogenetic tree manipulation supports calculating patristic distances, cophenetic distances, and Robinson-Foulds comparisons to evaluate tree topology and evolutionary relationships.
Yes, the system integrates with pandas and NumPy data ecosystems, allowing you to load BIOM-style feature tables and manipulate biological count data using standard data structures.
silversteinCompute sequence alignments, phylogenetic analyses, and microbial diversity statistics with scikit-bio.
Estrella-231Compute diversity, ordination, and statistical summaries from sequence-derived inputs.
rubenslivManipulate biological sequences and perform bioinformatics analyses in Python.
zongtingweiAutomate amplicon microbiome workflows from raw reads to abundance summaries.
