生物信息学

通往 bioSkills 和 ClawBio 提供的 400 多项生物信息学技能的大门。涵盖基因组学、转录组学、单细胞、变异检测、药物基因组学、宏基因组学、结构生物学等。按需获取特定领域的参考资料。

技能元数据

来源	可选 — 使用 hermes skills install official/research/bioinformatics 安装
路径	optional-skills/research/bioinformatics
版本	1.0.0
平台	linux, macos
标签	bioinformatics, genomics, sequencing, biology, research, science

参考：完整的 SKILL.md

信息

以下是 Hermes 在此技能被触发时加载的完整技能定义。这是智能体在技能激活时看到的指令。

生物信息学技能网关

当被问及生物信息学、基因组学、测序、变异检测、基因表达、单细胞分析、蛋白质结构、药物基因组学、宏基因组学、系统发育学或任何计算生物学任务时使用。

此技能是两个开源生物信息学技能库的网关。它没有捆绑数百个特定领域的技能，而是对它们建立索引，并按需获取您所需的内容。

来源

◆ bioSkills — 385 个参考技能（代码模式、参数指南、决策树） 仓库：https://github.com/GPTomics/bioSkills 格式：每个主题的 SKILL.md 文件，包含代码示例。支持 Python/R/CLI。

◆ ClawBio — 33 个可运行流程技能（可执行脚本、可复现性包） 仓库：https://github.com/ClawBio/ClawBio 格式：包含演示的 Python 脚本。每次分析导出 report.md + commands.sh + environment.yml。

如何获取和使用技能

1. 根据下面的索引确定领域和技能名称。
2. 克隆相关仓库（浅克隆以节省时间）：

   # bioSkills（参考材料）
   git clone --depth 1 https://github.com/GPTomics/bioSkills.git /tmp/bioSkills
   
   # ClawBio（可运行流程）
   git clone --depth 1 https://github.com/ClawBio/ClawBio.git /tmp/ClawBio

3. 读取特定技能：

   # bioSkills — 每个技能位于：<category>/<skill-name>/SKILL.md
   cat /tmp/bioSkills/variant-calling/gatk-variant-calling/SKILL.md
   
   # ClawBio — 每个技能位于：skills/<skill-name>/
   cat /tmp/ClawBio/skills/pharmgx-reporter/README.md

4. 将获取的技能作为参考材料使用。这些不是 Hermes 格式的技能 — 请将它们视为专家领域指南。它们包含正确的参数、适当的工具标志和经过验证的流程。

按领域划分的技能索引

序列基础

bioSkills: sequence-io/ — read-sequences, write-sequences, format-conversion, batch-processing, compressed-files, fastq-quality, filter-sequences, paired-end-fastq, sequence-statistics sequence-manipulation/ — seq-objects, reverse-complement, transcription-translation, motif-search, codon-usage, sequence-properties, sequence-slicing ClawBio: seq-wrangler — 序列质控、比对和 BAM 处理（封装 FastQC、BWA、SAMtools）

读长质控与比对

bioSkills: read-qc/ — quality-reports, fastp-workflow, adapter-trimming, quality-filtering, umi-processing, contamination-screening, rnaseq-qc read-alignment/ — bwa-alignment, star-alignment, hisat2-alignment, bowtie2-alignment alignment-files/ — sam-bam-basics, alignment-sorting, alignment-filtering, bam-statistics, duplicate-handling, pileup-generation

变异检测与注释

bioSkills: variant-calling/ — gatk-variant-calling, deepvariant, variant-calling (bcftools), joint-calling, structural-variant-calling, filtering-best-practices, variant-annotation, variant-normalization, vcf-basics, vcf-manipulation, vcf-statistics, consensus-sequences, clinical-interpretation ClawBio: vcf-annotator — VEP + ClinVar + gnomAD 注释，支持祖先感知上下文 variant-annotation — 变异注释流程

差异表达（批量 RNA-seq）

bioSkills: differential-expression/ — deseq2-basics, edger-basics, batch-correction, de-results, de-visualization, timeseries-de rna-quantification/ — alignment-free-quant (Salmon/kallisto), featurecounts-counting, tximport-workflow, count-matrix-qc expression-matrix/ — counts-ingest, gene-id-mapping, metadata-joins, sparse-handling ClawBio: rnaseq-de — 包含质控、归一化和可视化的完整差异表达流程 diff-visualizer — 为差异表达结果提供丰富的可视化和报告

单细胞 RNA-seq

bioSkills: single-cell/ — preprocessing, clustering, batch-integration, cell-annotation, cell-communication, doublet-detection, markers-annotation, trajectory-inference, multimodal-integration, perturb-seq, scatac-analysis, lineage-tracing, metabolite-communication, data-io ClawBio: scrna-orchestrator — 完整的 Scanpy 流程（质控、聚类、标记基因、注释） scrna-embedding — 基于 scVI 的潜在嵌入和批次整合

空间转录组学

bioSkills: spatial-transcriptomics/ — spatial-data-io, spatial-preprocessing, spatial-domains, spatial-deconvolution, spatial-communication, spatial-neighbors, spatial-statistics, spatial-visualization, spatial-multiomics, spatial-proteomics, image-analysis

表观基因组学

bioSkills: chip-seq/ — peak-calling, differential-binding, motif-analysis, peak-annotation, chipseq-qc, chipseq-visualization, super-enhancers atac-seq/ — atac-peak-calling, atac-qc, differential-accessibility, footprinting, motif-deviation, nucleosome-positioning methylation-analysis/ — bismark-alignment, methylation-calling, dmr-detection, methylkit-analysis hi-c-analysis/ — hic-data-io, tad-detection, loop-calling, compartment-analysis, contact-pairs, matrix-operations, hic-visualization, hic-differential ClawBio: methylation-clock — 表观遗传年龄估计

药物基因组学与临床

bioSkills: clinical-databases/ — clinvar-lookup, gnomad-frequencies, dbsnp-queries, pharmacogenomics, polygenic-risk, hla-typing, variant-prioritization, somatic-signatures, tumor-mutational-burden, myvariant-queries ClawBio: pharmgx-reporter — 基于 23andMe/AncestryDNA 的 PGx 报告（12 个基因，31 个 SNP，51 种药物） drug-photo — 药物照片 → 个性化 PGx 剂量卡（通过视觉） clinpgx — ClinPGx API，用于基因-药物数据和 CPIC 指南 gwas-lookup — 跨 9 个基因组数据库的联合变异查询 gwas-prs — 基于消费者遗传数据的多基因风险评分 nutrigx_advisor — 基于消费者遗传数据的个性化营养建议

群体遗传学与 GWAS

bioSkills: population-genetics/ — association-testing (PLINK GWAS), plink-basics, population-structure, linkage-disequilibrium, scikit-allel-analysis, selection-statistics causal-genomics/ — mendelian-randomization, fine-mapping, colocalization-analysis, mediation-analysis, pleiotropy-detection phasing-imputation/ — haplotype-phasing, genotype-imputation, imputation-qc, reference-panels ClawBio: claw-ancestry-pca — 基于 SGDP 参考面板的祖先 PCA 分析

宏基因组学与微生物组

bioSkills: metagenomics/ — kraken-classification, metaphlan-profiling, abundance-estimation, functional-profiling, amr-detection, strain-tracking, metagenome-visualization microbiome/ — amplicon-processing, diversity-analysis, differential-abundance, taxonomy-assignment, functional-prediction, qiime2-workflow ClawBio: claw-metagenomics — 鸟枪法宏基因组谱分析（分类、耐药组、功能通路）

基因组组装与注释

bioSkills: genome-assembly/ — hifi-assembly, long-read-assembly, short-read-assembly, metagenome-assembly, assembly-polishing, assembly-qc, scaffolding, contamination-detection genome-annotation/ — eukaryotic-gene-prediction, prokaryotic-annotation, functional-annotation, ncrna-annotation, repeat-annotation, annotation-transfer long-read-sequencing/ — basecalling, long-read-alignment, long-read-qc, clair3-variants, structural-variants, medaka-polishing, nanopore-methylation, isoseq-analysis

结构生物学与化学信息学

bioSkills: structural-biology/ — alphafold-predictions, modern-structure-prediction, structure-io, structure-navigation, structure-modification, geometric-analysis chemoinformatics/ — molecular-io, molecular-descriptors, similarity-searching, substructure-search, virtual-screening, admet-prediction, reaction-enumeration ClawBio: struct-predictor — 本地 AlphaFold/Boltz/Chai 结构预测与比较

蛋白质组学

bioSkills: proteomics/ — data-import, peptide-identification, protein-inference, quantification, differential-abundance, dia-analysis, ptm-analysis, proteomics-qc, spectral-libraries ClawBio: proteomics-de — 蛋白质组差异表达

通路分析与基因网络

bioSkills: pathway-analysis/ — go-enrichment, gsea, kegg-pathways, reactome-pathways, wikipathways, enrichment-visualization gene-regulatory-networks/ — scenic-regulons, coexpression-networks, differential-networks, multiomics-grn, perturbation-simulation

免疫信息学

bioSkills: immunoinformatics/ — mhc-binding-prediction, epitope-prediction, neoantigen-prediction, immunogenicity-scoring, tcr-epitope-binding tcr-bcr-analysis/ — mixcr-analysis, scirpy-analysis, immcantation-analysis, repertoire-visualization, vdjtools-analysis

CRISPR 与基因组工程

bioSkills: crispr-screens/ — mageck-analysis, jacks-analysis, hit-calling, screen-qc, library-design, crispresso-editing, base-editing-analysis, batch-correction genome-engineering/ — grna-design, off-target-prediction, hdr-template-design, base-editing-design, prime-editing-design

工作流管理

bioSkills: workflow-management/ — snakemake-workflows, nextflow-pipelines, cwl-workflows, wdl-workflows ClawBio: repro-enforcer — 将任何分析导出为可复现性包（Conda 环境 + Singularity + 校验和） galaxy-bridge — 访问来自 usegalaxy.org 的 8,000+ Galaxy 工具

专业领域

bioSkills: alternative-splicing/ — splicing-quantification, differential-splicing, isoform-switching, sashimi-plots, single-cell-splicing, splicing-qc ecological-genomics/ — edna-metabarcoding, landscape-genomics, conservation-genetics, biodiversity-metrics, community-ecology, species-delimitation epidemiological-genomics/ — pathogen-typing, variant-surveillance, phylodynamics, transmission-inference, amr-surveillance liquid-biopsy/ — cfdna-preprocessing, ctdna-mutation-detection, fragment-analysis, tumor-fraction-estimation, methylation-based-detection, longitudinal-monitoring epitranscriptomics/ — m6a-peak-calling, m6a-differential, m6anet-analysis, merip-preprocessing, modification-visualization metabolomics/ — xcms-preprocessing, metabolite-annotation, normalization-qc, statistical-analysis, pathway-mapping, lipidomics, targeted-analysis, msdial-preprocessing flow-cytometry/ — fcs-handling, gating-analysis, compensation-transformation, clustering-phenotyping, differential-analysis, cytometry-qc, doublet-detection, bead-normalization systems-biology/ — flux-balance-analysis, metabolic-reconstruction, gene-essentiality, context-specific-models, model-curation rna-structure/ — secondary-structure-prediction, ncrna-search, structure-probing

数据可视化与报告

bioSkills: data-visualization/ — ggplot2-fundamentals, heatmaps-clustering, volcano-customization, circos-plots, genome-browser-tracks, interactive-visualization, multipanel-figures, network-visualization, upset-plots, color-palettes, specialized-omics-plots, genome-tracks reporting/ — rmarkdown-reports, quarto-reports, jupyter-reports, automated-qc-reports, figure-export ClawBio: profile-report — 分析报告 data-extractor — 从科学图像中提取数值数据（通过视觉） lit-synthesizer — PubMed/bioRxiv 搜索、总结、引用图谱 pubmed-summariser — 基因/疾病 PubMed 搜索，生成结构化简报

数据库访问

bioSkills: database-access/ — entrez-search, entrez-fetch, entrez-link, blast-searches, local-blast, sra-data, geo-data, uniprot-access, batch-downloads, interaction-databases, sequence-similarity ClawBio: ukb-navigator — 跨 12,000+ UK Biobank 字段的语义搜索 clinical-trial-finder — 临床试验发现

实验设计

bioSkills: experimental-design/ — power-analysis, sample-size, batch-design, multiple-testing

组学机器学习

bioSkills: machine-learning/ — omics-classifiers, biomarker-discovery, survival-analysis, model-validation, prediction-explanation, atlas-mapping ClawBio: claw-semantic-sim — 疾病文献的语义相似性指数（PubMedBERT） omics-target-evidence-mapper — 跨组学来源汇总靶点水平证据

环境设置

这些技能假定使用生物信息学工作站。常见依赖项：

# Python
pip install biopython pysam cyvcf2 pybedtools pyBigWig scikit-allel anndata scanpy mygene

# R/Bioconductor
Rscript -e 'BiocManager::install(c("DESeq2","edgeR","Seurat","clusterProfiler","methylKit"))'

# 命令行工具 (Ubuntu/Debian)
sudo apt install samtools bcftools ncbi-blast+ minimap2 bedtools

# 命令行工具 (macOS)
brew install samtools bcftools blast minimap2 bedtools

# 或者通过 Conda 安装（推荐用于可复现性）
conda install -c bioconda samtools bcftools blast minimap2 bedtools fastp kraken2

注意事项

• 获取的技能不是 Hermes SKILL.md 格式。它们使用自己的结构（bioSkills：代码模式食谱；ClawBio：README + Python 脚本）。请将其作为专家参考材料阅读。
• bioSkills 是参考指南——它们展示了正确的参数和代码模式，但不是可执行的流程。
• ClawBio 技能是可执行的——许多技能具有 --demo 标志，可以直接运行。
• 两个仓库都假定已安装生物信息学工具。在运行流程之前，请检查先决条件。
• 对于 ClawBio，首先在被克隆的仓库中运行 pip install -r requirements.txt。
• 基因组数据文件可能非常大。下载参考基因组、SRA 数据集或构建索引时，请注意磁盘空间。