GPTomics/bioSkills

Registry 信息

项目简介

一套SKILLS.md文档，提供使用Claude Skill进行生物信息学分析的指南。涵盖从数据预处理到高级分析的完整工作流程，包括序列比对、变异检测、表达分析和可视化。

要点

• 全面的生物信息学工作流程指导
• 涵盖数据预处理、比对和变异检测
• 包含表达分析和可视化技术
• 提供最佳实践和故障排除技巧
• 专注于可重复分析和文档记录

使用场景

• RNA-Seq差异表达分析
• WES/WGS变异检测与注释
• 序列数据质量控制与预处理
• 基因组数据可视化与解读
• 构建可重复的生物信息学流程

README 摘要

# bioSkills A collection of skills that guide AI coding agents (Claude Code, OpenAI Codex, Google Gemini, OpenCode, OpenClaw) through common bioinformatics tasks. ## Project Goal This repository provides AI agents with expert knowledge for bioinformatics workflows. Each skill contains code patterns, best practices, and examples that help agents generate correct, idiomatic code for common tasks. Target users range from undergrads learning computational biology to PhD researchers processing large-scale data. The skills cover the full spectrum from basic sequence manipulation to advanced analyses like single-cell RNA-seq and population genetics. ## Performance Evaluation summary report available at [bioskills_eval_20260328.pdf](resources/bioskills_eval_20260328.pdf). Evaluations were performed on the [Bio-Task Bench](https://github.com/GPTomics/bioTaskBench) dataset.  ## Requirements ### Python - Python 3.9+ - biopython, pysam, cyvcf2, pybedtools, pyBigWig, scikit-allel, anndata ```bash pip install biopython pysam cyvcf2 pybedtools pyBigWig scikit-allel anndata mygene ``` ### R/Bioconductor Required for differential expression, single-cell, pathway analysis, and methylation skills. ```r if (!require('BiocManager', quietly = TRUE)) install.packages('BiocManager') BiocManager::install(c('DESeq2', 'edgeR', 'Seurat', 'clusterProfiler', 'methylKit')) ``` ### CLI Tools ```bash # macOS brew install samtools bcftools blast minimap2 bedtools # Ubuntu/Debian sudo apt install samtools bcftools ncbi-blast+ minimap2 bedtools # conda conda install -c bioconda samtools bcftools blast minimap2 bedtools \ fastp kraken2 metaphlan sra-tools bwa-mem2 bowtie2 star hisat2 \ manta delly cnv

话题

暂无话题