An agentic skills framework & software development methodology that works.

Annotate and review coding agent plans and code diffs visually, share with your team, send feedback to agents with one click.

Contextual AI models for single-cell protein biology

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly…

Python toolkit for LC-MS/MS Proteomics analysis based on MuData

Skills for Real Engineers. Straight from my .claude directory.

Light, fluffy, and always free - The AWS Local Emulator alternative

Automated RNA-seq downstream analysis framework for differential expression, visualization, GO enrichment, and HTML reporting in R.

A repository of datasets in ProteomeXchange annotated in SDRF, previously part of the specification

Agent Lattice: a knowledge graph for your codebase, written in markdown.

AI tooling and documentation for ProteoWizard/Skyline development

This repository defines a prompt context framework providing epistemic grounding for vibe-coded software tools in proteomics.

Metabolomics Standards Initiative Ontology

Parser to get meta information from mzML file and parse relevant information to a ISA-Tab structure

This is the development repository for the STATistics Ontology (STATO). For more information and demonstration on the ontology content, please visit its website:

Download and Convert METASPACE datasets to common formats such as AnnData or SpatialData

Links between modalities in mudata

A single CLAUDE.md file to improve Claude Code behavior, derived from Andrej Karpathy's observations on LLM coding pitfalls.

Deciphering the Complexity of Spatial-Temporal Transcriptomic and Proteomics via Subcellular Location Optimal Transport(SLOT)

yq is a portable command-line YAML, JSON, XML, CSV, TOML, HCL and properties processor

Generate beautiful dark-themed system architecture diagrams as standalone HTML/SVG files. Works as a Claude AI skill.

A large open benchmark data resource for computational proteomics

Nanoneedles Enable Spatiotemporal Lipidomics of Living Tissues