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a set of SKILLS.md for doing bioinformatics with agents like claude code
| Date | Stars |
|---|---|
| 2026-07-31 | 1099 |
| 2026-08-01 | 1105 |
| 2026-08-06 | 1105 |
Today
— stars today
This week
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This month
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Momentum
5.0
growth rate 0.00%/day
# 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 cnvkit macs3 macs2 genrich tobias rgt-hint idr picard \
preseq deeptools chromap subread fithichip gatk4
```
## Installation
### Claude Code
```bash
git clone [email protected]:GPTomics/bioSkills.git
cd bioSkills
./install-claude.sh # Install globally
./install-claude.sh --project /path/to/project # Or install to specific project
./install-claude.sh --categories "single-cell,variant-calling" # Install specific categories
./install-claude.sh --list # List available skills
./install-claude.sh --validate # Validate all skills
./install-claude.sh --update # Only update changed skills
./install-claude.sh --uninstall # Remove all bio-* skills
```
### Codex CLI
```bash
./install-codex.sh # Install globally
./install-codex.sh --project /path/to/project # Or install to specific project
./install-codex.sh --categories "single-cell,variant-calling" # Install specific categories
./install-codex.sh --list # List available skills
./install-codex.sh --validate # Validate all skills
./install-codex.sh --update # Only update changed skills
./install-codex.sh --uninstall # Remove all bio-* skills
```
### Antigravity CLI
Antigravity CLI replaces Gemini CLI (sunset 2026-06-18) and uses the open Agent Skills standard. Global installs land at `~/.gemini/antigravity/skills/`; project installs land at `.agents/skills/`.
```bash
./install-antigravity.sh # Install globally
./install-antigravity.sh --project /path/to/project # Or install to specific project
./install-antigravity.sh --categories "single-cell,variant-calling" # Install specific categories
./install-antigravity.sh --list # List available skills
./install-antigravity.sh --validate # Validate all skills
./install-antigravity.sh --update # Only update changed skills
./install-antigravity.sh --uninstall # Remove all bio-* skills
```
### OpenCode
```bash
./install-opencode.sh Excerpt of 40,417 characters
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Bap · Tessl.io · United Kingdom
1
Would you bet a product on this? Bounded 0–100 and slow moving.
matched fp:e0f1982ac80aa30c, desc:bioinformatics