bioSkills Installer
Meta-skill that installs the full bioSkills collection (425 skills across 62 categories) for bioinformatics analysis.
Installation
Run the bundled install script to download and install all bioSkills:
CODEBLOCK0
Or install only specific categories:
CODEBLOCK1
What Gets Installed
| Category Group | Categories | Skills |
|---|
| Sequence & Alignment | sequence-io, sequence-manipulation, alignment, alignment-files, database-access | 40 |
| Read Processing |
read-qc, read-alignment | 11 |
| RNA-seq & Expression | differential-expression, rna-quantification, expression-matrix | 14 |
| Single-Cell & Spatial | single-cell, spatial-transcriptomics | 25 |
| Variant Analysis | variant-calling, copy-number, phasing-imputation | 21 |
| Epigenomics | chip-seq, atac-seq, methylation-analysis, hi-c-analysis | 25 |
| Metagenomics & Microbiome | metagenomics, microbiome | 13 |
| Genomics & Assembly | genome-assembly, genome-annotation, genome-intervals, genome-engineering, primer-design | 29 |
| Regulatory & Causal | gene-regulatory-networks, causal-genomics, rna-structure | 13 |
| Temporal & Ecological | temporal-genomics, ecological-genomics | 11 |
| Immunology & Clinical | immunoinformatics, clinical-databases, tcr-bcr-analysis, epidemiological-genomics | 25 |
| Specialized Omics | proteomics, metabolomics, alternative-splicing, chemoinformatics, liquid-biopsy | 36 |
| RNA Biology | small-rna-seq, epitranscriptomics, clip-seq, ribo-seq | 20 |
| Phylogenetics & Evolution | phylogenetics, population-genetics, comparative-genomics | 16 |
| Structural & Systems | structural-biology, systems-biology | 11 |
| Screens & Cytometry | crispr-screens, flow-cytometry, imaging-mass-cytometry | 22 |
| Pathway & Integration | pathway-analysis, multi-omics-integration, restriction-analysis | 14 |
| Infrastructure | data-visualization, machine-learning, workflow-management, reporting, experimental-design, long-read-sequencing | 39 |
| Workflows | End-to-end pipelines (FASTQ to results) | 40 |
After Installation
Once installed, skills are automatically triggered based on the task at hand. Example requests:
- - "I have RNA-seq counts from treated vs control samples - find the differentially expressed genes"
- "Call variants from this whole genome sequencing BAM file"
- "Cluster my single-cell RNA-seq data and find marker genes"
- "Predict the structure of this protein sequence"
- "Run a metagenomics classification on these shotgun reads"
Source
GitHub: https://github.com/GPTomics/bioSkills
Related Skills
After installation, 425 individual skills become available across these categories:
sequence-io, sequence-manipulation, database-access, alignment, alignment-files,
variant-calling, phylogenetics, differential-expression, structural-biology,
single-cell, pathway-analysis, restriction-analysis, methylation-analysis,
chip-seq, metagenomics, long-read-sequencing, read-qc, read-alignment,
rna-quantification, genome-assembly, genome-intervals, data-visualization,
expression-matrix, copy-number, proteomics, flow-cytometry, population-genetics,
multi-omics-integration, spatial-transcriptomics, machine-learning,
workflow-management, microbiome, metabolomics, phasing-imputation,
primer-design, hi-c-analysis, imaging-mass-cytometry, atac-seq,
crispr-screens, reporting, experimental-design, clinical-databases,
tcr-bcr-analysis, small-rna-seq, epitranscriptomics, clip-seq, ribo-seq,
genome-engineering, systems-biology, epidemiological-genomics,
immunoinformatics, comparative-genomics, alternative-splicing,
chemoinformatics, liquid-biopsy, genome-annotation, gene-regulatory-networks,
causal-genomics, rna-structure, temporal-genomics, ecological-genomics, workflows
bioSkills 安装程序
用于生物信息学分析的元技能，可安装完整的 bioSkills 集合（涵盖 62 个类别中的 425 项技能）。
安装
运行捆绑的安装脚本以下载并安装所有 bioSkills：
bash
bash scripts/install-bioskills.sh
或仅安装特定类别：
bash
bash scripts/install-bioskills.sh --categories single-cell,variant-calling,differential-expression
安装内容
| 类别组 | 类别 | 技能数 |
|---|
| 序列与比对 | 序列输入输出、序列操作、比对、比对文件、数据库访问 | 40 |
| 读段处理 |
读段质量控制、读段比对 | 11 |
| RNA-seq 与表达 | 差异表达、RNA 定量、表达矩阵 | 14 |
| 单细胞与空间 | 单细胞、空间转录组学 | 25 |
| 变异分析 | 变异检测、拷贝数、定相与插补 | 21 |
| 表观基因组学 | ChIP-seq、ATAC-seq、甲基化分析、Hi-C 分析 | 25 |
| 宏基因组学与微生物组 | 宏基因组学、微生物组 | 13 |
| 基因组学与组装 | 基因组组装、基因组注释、基因组区间、基因组工程、引物设计 | 29 |
| 调控与因果 | 基因调控网络、因果基因组学、RNA 结构 | 13 |
| 时间与生态 | 时间基因组学、生态基因组学 | 11 |
| 免疫学与临床 | 免疫信息学、临床数据库、TCR/BCR 分析、流行病学基因组学 | 25 |
| 专业组学 | 蛋白质组学、代谢组学、可变剪接、化学信息学、液体活检 | 36 |
| RNA 生物学 | 小 RNA-seq、表观转录组学、CLIP-seq、Ribo-seq | 20 |
| 系统发育与进化 | 系统发育学、群体遗传学、比较基因组学 | 16 |
| 结构与系统 | 结构生物学、系统生物学 | 11 |
| 筛选与细胞术 | CRISPR 筛选、流式细胞术、成像质谱流式 | 22 |
| 通路与整合 | 通路分析、多组学整合、限制性分析 | 14 |
| 基础设施 | 数据可视化、机器学习、工作流管理、报告、实验设计、长读段测序 | 39 |
| 工作流 | 端到端流程（FASTQ 到结果） | 40 |
安装后
安装完成后，技能会根据当前任务自动触发。示例请求：
- - 我有处理组与对照组的 RNA-seq 计数数据——找出差异表达基因
- 对此全基因组测序 BAM 文件进行变异检测
- 对我的单细胞 RNA-seq 数据进行聚类并寻找标记基因
- 预测此蛋白质序列的结构
- 对这些鸟枪法测序读段进行宏基因组分类
来源
GitHub：https://github.com/GPTomics/bioSkills
相关技能
安装后，以下类别的 425 项独立技能将可用：
序列输入输出、序列操作、数据库访问、比对、比对文件、
变异检测、系统发育学、差异表达、结构生物学、
单细胞、通路分析、限制性分析、甲基化分析、
ChIP-seq、宏基因组学、长读段测序、读段质量控制、读段比对、
RNA 定量、基因组组装、基因组区间、数据可视化、
表达矩阵、拷贝数、蛋白质组学、流式细胞术、群体遗传学、
多组学整合、空间转录组学、机器学习、
工作流管理、微生物组、代谢组学、定相与插补、
引物设计、Hi-C 分析、成像质谱流式、ATAC-seq、
CRISPR 筛选、报告、实验设计、临床数据库、
TCR/BCR 分析、小 RNA-seq、表观转录组学、CLIP-seq、Ribo-seq、
基因组工程、系统生物学、流行病学基因组学、
免疫信息学、比较基因组学、可变剪接、
化学信息学、液体活检、基因组注释、基因调控网络、
因果基因组学、RNA 结构、时间基因组学、生态基因组学、工作流
