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"生物信息学 — 来自 bioSkills 和 ClawBio 的 400+ 生物信息学技能网关"
生物信息学
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 SKILL.md
信息
生物信息学技能网关
来源
仓库：https://github.com/GPTomics/bioSkills
格式：每个主题一个 SKILL.md，含代码示例。支持 Python/R/CLI。
仓库：https://github.com/ClawBio/ClawBio
格式：带演示的 Python 脚本。每次分析导出 report.md + commands.sh + environment.yml。
如何获取并使用技能
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按领域划分的技能索引
序列基础
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、比对与 BAM 处理（封装 FastQC、BWA、SAMtools）
读段质控与比对
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
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 — 结合祖先背景的 VEP + ClinVar + gnomAD 注释
variant-annotation — 变异注释流程
差异表达（Bulk RNA-seq）
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 — 含质控、归一化和可视化的完整差异表达流程
diff-visualizer — 差异表达结果的丰富可视化与报告
单细胞 RNA-seq
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 Scanpy 流程（质控、聚类、标记基因、注释）
scrna-embedding — 基于 scVI 的潜在嵌入与批次整合
空间转录组学
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
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 — 表观遗传年龄估算
药物基因组学与临床
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（通过视觉识别）
clinpgx — 用于基因-药物数据和 CPIC 指南的 ClinPGx API
gwas-lookup — 跨 9 个基因组数据库的联合变异查询
gwas-prs — 基于消费者基因数据的多基因风险评分
nutrigx_advisor — 基于消费者基因数据的个性化营养建议
群体遗传学与 GWAS
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
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 — 鸟枪法宏基因组分析（分类、耐药组、功能通路）
基因组组装与注释
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
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
proteomics/ — data-import, peptide-identification, protein-inference, quantification, differential-abundance, dia-analysis, ptm-analysis, proteomics-qc, spectral-libraries
ClawBio:
proteomics-de — 蛋白质组学差异表达分析
通路分析与基因网络
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
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
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
workflow-management/ — snakemake-workflows, nextflow-pipelines, cwl-workflows, wdl-workflows
ClawBio:
repro-enforcer — 将任意分析导出为可复现性包（Conda 环境 + Singularity + 校验和）
galaxy-bridge — 访问 usegalaxy.org 上的 8,000+ Galaxy 工具
专业领域
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
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 — 分析概况报告
data-extractor — 从科学图像中提取数值数据（通过视觉识别）
lit-synthesizer — PubMed/bioRxiv 检索、摘要与引用图谱
pubmed-summariser — 基因/疾病 PubMed 检索与结构化简报
数据库访问
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
experimental-design/ — power-analysis, sample-size, batch-design, multiple-testing
组学机器学习
machine-learning/ — omics-classifiers, biomarker-discovery, survival-analysis, model-validation, prediction-explanation, atlas-mapping
ClawBio:
claw-semantic-sim — 疾病文献语义相似度索引（PubMedBERT）
omics-target-evidence-mapper — 跨组学来源的靶点级证据聚合
环境配置
注意事项
--demo 标志，可直接运行。pip install -r requirements.txt。