scikit-bio
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
npx skills add LeonChaoX/qinyan-academic-skills --skill scikit-bio --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# scikit-bio ## Overview scikit-bio is a comprehensive Python library for working with biological data. Apply this skill for bioinformatics analyses spanning sequence manipulation, alignment, phylogenetics, microbial ecology, and multivariate statistics. ## When to Use This Skill This skill should be used when the user: - Works with biological sequences (DNA, RNA, protein) - Needs to read/write biological file formats (FASTA, FASTQ, GenBank, Newick, BIOM, etc.) - Performs sequence alignments or searches for motifs - Constructs or analyzes phylogenetic trees - Calculates diversity metrics (alpha/beta diversity, UniFrac distances) - Performs ordination analysis (PCoA, CCA, RDA) - Runs statistical tests on biological/ecological data (PERMANOVA, ANOSIM, Mantel) - Analyzes microbiome or community ecology data - Works with protein embeddings from language models - Needs to manipulate biological data tables ## Core Capabilities ### 1. Sequence Manipulation Work with biological sequences using specialized classes for DNA, RNA, and protein data. **Key operations:** - Read/write sequences from FASTA, FASTQ, GenBank, EMBL formats - Sequence slicing, concatenation, and searching - Reverse comp
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Sequence Manipulation
- 2. Sequence Alignment
- 3. Phylogenetic Trees
- 4. Diversity Analysis
- 5. Ordination Methods
- 6. Statistical Testing
- 7. File I/O and Format Conversion
- 8. Distance Matrices
- 9. Biological Tables
- 10. Protein Embeddings
- Best Practices
uv pip install scikit-bio
What does the scikit-bio skill do?
Biological data toolkit. Sequence analysis, alignments, phylogenetic trees, diversity metrics (alpha/beta, UniFrac), ordination (PCoA), PERMANOVA, FASTA/Newick I/O, for microbiome analysis.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill scikit-bio --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.