Habilidades scikit-bio
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scikit-bio

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使用 scikit-bio 分析生物数据

Também disponível em: davila7

处理生物序列，计算多样性指标，并对微生物组和生态数据执行统计检验。本技能提供生物信息学工作流的全面指导，包括序列比对、系统发育分析和排序分析。

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A utilizar "scikit-bio". Calculate diversity metrics from my OTU table

Resultado esperado:

  • Read your BIOM table: Table.read('table.biom')
  • Calculate alpha diversity: alpha_diversity('shannon', counts, ids=sample_ids)
  • Calculate beta diversity: beta_diversity('braycurtis', counts, ids=sample_ids)
  • Run PERMANOVA: permanova(distance_matrix, grouping, permutations=999)

A utilizar "scikit-bio". Build a phylogenetic tree from my sequences

Resultado esperado:

  • Read sequences from FASTA: skbio.DNA.read('sequences.fasta')
  • Calculate distance matrix: seq1.distance(seq2) or use kmer_distance
  • Build tree with NJ: nj(distance_matrix)
  • Calculate Robinson-Foulds distance: tree.robinson_foulds(other_tree)

Auditoria de Segurança

Seguro
v4 • 1/17/2026

Documentation-only skill with no executable code. All 133 static findings are false positives: detected backticks are markdown code delimiters, C2 keywords are scientific abbreviations (PC1, CCA, RDA for ordination methods), weak crypto flags are biological substitution matrices (BLOSUM62 for protein alignments), and URLs are official documentation links. No command injection, network exfiltration, or malicious patterns exist.

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⚙️ Comandos externos (5)
SKILL.md:44-61 SKILL.md:64-65 SKILL.md:78-81 references/api_reference.md:20-35 references/api_reference.md:39-52
🌐 Acesso à rede (1)
SKILL.md:432-434
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Pontuação de qualidade

41
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Manutenibilidade
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Conteúdo
20
Comunidade
100
Segurança
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Conformidade com especificações

O Que Você Pode Construir

分析微生物组多样性

从 OTU 表计算 alpha 和 beta 多样性，并对样本分组执行 PERMANOVA 检验。

构建系统发育树

从序列比对构建树，并计算 Robinson-Foulds 距离以进行树比较。

处理序列数据

在 19+ 种文件格式中读取、过滤和转换生物序列，并进行验证。

Tente Estes Prompts

基础序列操作 
Show me how to read a FASTA file with skbio, calculate reverse complement, and find motifs using regex patterns.
多样性分析 
Guide me through calculating Shannon alpha diversity from a counts matrix and computing Bray-Curtis beta diversity between samples.
系统发育分析 
Help me build a phylogenetic tree using Neighbor Joining from a distance matrix and calculate patristic distances between taxa.
统计检验 
Show me how to run a PERMANOVA test on a distance matrix to determine if sample groups differ significantly, with 999 permutations.

Melhores Práticas

  • 对大型序列文件使用生成器（skbio.io.read）以避免内存问题
  • 与 pandas 和 numpy 集成以进行下游分析和可视化
  • 在计算多样性之前验证各文件中的序列 ID 匹配

Evitar

  • 不要对计数使用相对频率——先转换为整数
  • 在计算 Robinson-Foulds 距离时不要混用有根树和无根树
  • 运行 PERMANOVA 时不要跳过 PERMDISP——检查离散性假设

Perguntas Frequentes

scikit-bio 支持哪些文件格式？
FASTA、FASTQ、GenBank、EMBL、Clustal、PHYLIP、Stockholm、Newick、BIOM（HDF5/JSON）和分隔矩阵。
如何计算系统发育多样性？
Use alpha_diversity('faith_pd', counts, tree=tree, otu_ids=feature_ids) with a rooted phylogenetic tree.
alpha 多样性与 beta 多样性有什么区别？
Alpha 衡量样本内多样性（例如 Shannon、Simpson），beta 衡量样本间差异（例如 Bray-Curtis、UniFrac）。
我可以将 scikit-bio 与 QIIME 2 一起使用吗？
是的，scikit-bio 读取并写入与 QIIME 2 兼容的格式，包括 BIOM 表、树和距离矩阵。
如何高效处理大型序列文件？
Use generator-based reading: for seq in skbio.io.read('large.fasta', format='fasta', constructor=skbio.DNA)
生态数据有哪些可用的统计检验？
PERMANOVA、ANOSIM、PERMDISP、Mantel test 和 Bioenv 用于环境变量选择。

Detalhes do Desenvolvedor

Licença

BSD-3-Clause license

Repositório

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/scikit-bio

Referência

main

Estrutura de arquivos

📁 references/

📄 api_reference.md

📄 SKILL.md