scikit-bio SKILL.md skillA
scikit-bio from jaechang-hits/sciagent-skills is an agent skill: a SKILL.md folder an AI agent loads when a task calls for it.
mdr add jaechang-hits/sciagent-skills/scikit-bio@git:20260428.81ea2d2Pins git:20260428.81ea2d2 in mdr.lock. Pin the fingerprint instead.
- Audit grade
- A, 17 of 17 checks passed
- Kind
- SKILL.md skill
- Repository
- jaechang-hits/sciagent-skills
- Path
skills/genomics-bioinformatics/scikit-bio/SKILL.md- Versions recorded
- 2
- Latest version
- git:20260428.81ea2d2, committed Apr 28, 2026
- First version recorded
- Feb 18, 2026
- Size
- 17,721 bytes
- Repository stars
- 381
- License
- a license file GitHub does not identify
Python library for biology: sequence manipulation (DNA/RNA/protein), pairwise/multiple alignment, phylogenetic trees (NJ, UPGMA), diversity (Shannon, Faith PD, Bray-Curtis, UniFrac), ordination (PCoA, CCA, RDA), stats (PERMANOVA, ANOSIM, Mantel), file I/O (FASTA, FASTQ, Newick, BIOM). Use for microbiome, community ecology, or phylogenetics.
Collected from public GitHub. Every version is saved exactly as it was and never changes. Install it at an exact version with the mdr tool, and every file is checked before it reaches your agent. The main file is checked against the SHA-256 fingerprint recorded here, and the others against the fingerprints GitHub keeps for its source commit. The automatic checks below grade the latest version, and the same checks always give the same file the same grade.
What the file says
# scikit-bio ## Overview scikit-bio is a comprehensive Python library for biological data analysis, spanning sequence manipulation, alignment, phylogenetics, microbial ecology, and multivariate statistics. It provides specialized data structures (DNA, RNA, Protein, DistanceMatrix, TreeNode, TabularMSA) that integrate with the broader Python scientific stack. ## When to Use - Calculating alpha/beta diversity and running PERMANOVA on microbiome data - Building phylogenetic trees from distance matrices (NJ, UPGMA) - Performing PCoA ordination on community composition data - Reading/writing biological formats (FASTA, FASTQ, Newick, BIOM) - Pairwise sequence alignment (Smith-Waterman, Needleman-Wunsch) - Computing UniFrac distances for phylogenetic beta diversity - Statistical testing on ecological distance matrices (ANOSIM, Mantel) - Working with QIIME 2 artifacts and microbiome pipelines - For high-throughput NGS alignment/variant calling, use STAR/BWA instead - For protein structure prediction, use AlphaFold/ESMFold instead ## Prerequisites ```bash pip install scikit-bio # Optional: pip install biom-format — HDF5 BIOM table support …
Read the whole file at its exact version.
How to install
mdr add jaechang-hits/sciagent-skills/scikit-bio@sha256:4ef9661d1e003968The line at the top of this page pins the label git:20260428.81ea2d2, which is what most people want. This one pins the sha256 fingerprint of the contents instead, so it survives a label being moved. Either way the exact version is written to mdr.lock, and mdr install downloads and checks those contents again, so it installs them exactly or stops with an error.
[](https://markdownregistry.com/a/art_tghz7inumluotc36)
2 badge image fetches in 30 days. What the badge shows.
Versions
The registry has recorded 2 versions of this file, between Feb 18, 2026 and Apr 28, 2026, about one every 69 days.
| version | committed | commit | size | audit | |
|---|---|---|---|---|---|
| git:20260428.81ea2d2 latest | 2026-04-28 | 81ea2d2 | 17,721 B | A | view · diff |
| git:20260218.8df1694 | 2026-02-18 | 8df1694 | 17,855 B | A | view |
Audit of the latest version
- pass: Frontmatter block present
- pass: Frontmatter declares a name
- pass: Frontmatter declares a description
- pass: Size between 200 bytes and 200 KB (17721 bytes)
- pass: No zero-width or bidi control characters
- pass: No instruction hidden inside an HTML comment
- pass: No link to an exfiltration or paste host
- pass: No credential-shaped string
- pass: No instruction to send local credentials anywhere
- pass: No text hidden with inline styles
- pass: No prompt-injection phrasing
- pass: No curl or wget piped into a shell
- pass: No recursive delete of root, home or parent
- pass: No instruction to read or print local credentials
- pass: No base64 blob over 200 characters
- pass: No link to a raw IP address
- pass: No script tag
Source
jaechang-hits/sciagent-skills · 381 stars · license a license file GitHub does not identify · pushed 2026-10-16 · branch main
API
GET https://markdownregistry.com/api/v1/artifacts/art_tghz7inumluotc36 GET https://markdownregistry.com/api/v1/resolve?ref=jaechang-hits/sciagent-skills/scikit-bio GET https://markdownregistry.com/api/v1/blob/4ef9661d1e0039689fd88ec1ca65b23114e73ef3bb96759f02415c7d7aed07db
Your AI assistant does the legwork. You hear about the deals worth your word. Hand yours the standing instructions at modelranch.com and it joins the network that reads files like this one.
Guides: the SKILL.md format and its required fields · what to check before you install a skill · how to pin a skill to an exact version · where to find agent skills · keeping a team on the same skills · which agent file does what.
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