sciagent-skills

SciAgent-Skills

Turn your AI coding agent into a life sciences expert — 199 bioinformatics skills for Claude Code covering RNA-seq, single-cell analysis, genomics, proteomics, drug discovery, and more. Boosted BixBench from 65% to 92%. Open source.

SciAgent-Skills is the largest open-source skill library for scientific AI agents. It equips Claude Code (and any markdown-compatible agent) with domain-specific knowledge for computational biology, bioinformatics, cheminformatics, and biostatistics — no fine-tuning required, just plug in and analyze.

Keywords: bioinformatics AI agent, Claude Code skills, scientific computing, RNA-seq analysis, single-cell RNA-seq, drug discovery pipeline, protein structure prediction, computational biology tools, life science automation, BixBench benchmark

Benchmark: 92.0% on BixBench-Verified-50

BixBench is a benchmark for evaluating AI agents on real-world bioinformatics tasks. SciAgent-Skills achieved 92.0% accuracy on BixBench-Verified-50, the highest among all tested systems:

System	BixBench-Verified-50 Accuracy
Claude Code (Opus 4.6) + SciAgent-Skills	92.0%
Claude Code (Opus 4.6) baseline	65.3%

Simply equipping Claude Code with these domain-specific skills yields a +26.7 percentage point improvement — no fine-tuning, no custom model, just structured scientific knowledge.

Try It Now — OmicsHorizon

Want to try these skills without any setup? OmicsHorizon (오믹스 호라이즌) is the web platform powered by SciAgent-Skills. Sign up and start analyzing your bioinformatics data directly in your browser — RNA-seq, proteomics, drug screening, and more.

---

199 ready-to-use scientific skills for AI coding agents — covering genomics, proteomics, drug discovery, biostatistics, scientific computing, and scientific writing.

Each skill is a self-contained SKILL.md file with runnable code examples, key parameters, troubleshooting guides, and best practices. Designed for Claude Code, but compatible with any AI agent that reads markdown skill files (setup guides below).

What's Inside

Category	Skills	Examples
Genomics & Bioinformatics	65	Scanpy, BioPython, pysam, gget, KEGG, PubMed, scvi-tools, Bakta, Roary
Structural Biology & Drug Discovery	26	RDKit, AutoDock Vina, ChEMBL, PDB, DeepChem, datamol
Scientific Computing	24	Polars, Dask, NetworkX, SymPy, UMAP, PyG, Zarr, SimPy
Cell Biology	15	pydicom, histolab, FlowIO
Biostatistics	12	scikit-learn, statsmodels, PyMC, SHAP, survival analysis
Scientific Writing	21	Manuscript writing, peer review, LaTeX posters, slides, figure guides
Systems Biology & Multi-omics	11	COBRApy, LaminDB, Reactome, STRING
Proteomics & Protein Engineering	10	ESM, UniProt, PyOpenMS, matchms, HMDB
Lab Automation	6	Opentrons, Benchling
Data Visualization	5	Plotly, Seaborn
Molecular Biology	3	CRISPR sgRNA design, gene expression, cloning

Skill types: 72 toolkits, 53 database connectors, 37 guides, 37 pipelines

Installation

Prerequisites

• An AI coding agent: Claude Code, OpenAI Codex CLI, Cursor, or Windsurf
• Git
• Python 3.12+ (only needed if you want to run validation scripts)

Note: SciAgent-Skills is not an npm package. Skills are plain markdown files read directly by your AI agent — no npx, npm install, or runtime dependencies needed. Just clone the repository and point your agent at the skill files.

Step 1: Clone the Repository

git clone https://github.com/jaechang-hits/SciAgent-Skills.git
cd SciAgent-Skills

Step 2: Choose Your Setup Method

Method A: Claude Code Plugin (Recommended)

Load SciAgent-Skills as a Claude Code plugin for the current session: