michael-denyer/pstack-claude
Claude Code, Codex, OpenCode, Gemini, and Prime Agent versions of Poteto's pstack. Rigorous agent workflows with Cursor primitives translated for other harnesses.
Software Engineer and Bioinformatician
Repositories
michael-denyer/agent-formal-verify
TLA+ model checking and Lean proofs for coding agents, with explicit tool setup.
michael-denyer/fast-beagle-5.5
Fast standalone C port of Beagle 5.5 genotype phasing and imputation, byte-identical output to the Java release.
michael-denyer/fast-beagle-5.4
C port of Beagle 5.4 (29Oct24.c8e) with byte-identical VCF output and BGEN extensions
michael-denyer/michael-denyer
My GitHub profile
michael-denyer/memory-mcp
Engram-inspired memory MCP server with hot cache and pattern mining
michael-denyer/jamma
JAMMA (Highly-Accelerated Multi-method Mixed-model Association) -- a fast and modern Python and C reimplementation of GEMMA for large-scale GWAS.
michael-denyer/jamma-lean-proofs
michael-denyer/bioconda-recipes
Conda recipes for the bioconda channel.
michael-denyer/numpy-mkl
MKL-accelerated NumPy and SciPy wheels
michael-denyer/claude-mem-lean
Persistent Context Across Sessions for Every Agent – Captures everything your agent does during sessions, compresses it with AI, and injects relevant context back into future sessions. Works with Claude Code, OpenClaw, Codex, Gemini, Hermes, Copilot, OpenCode + More
michael-denyer/pyLocusZoom
pyLocusZoom -- publication-ready GWAS visualization in Python: LocusZoom-style regional association plots with LD coloring, gene tracks and recombination overlays, plus Manhattan, QQ, Miami, eQTL, fine-mapping, PheWAS and forest plots. Dog and cat genomes built in.
michael-denyer/bonsai-agent
Claude Code subagent that runs tasks on a local Bonsai 2 27B model via the PrismML MLX fork, with an auto-starting server
michael-denyer/michael-denyer.github.io
The Aether Works — steampunk landing page, run by cats, powered by commits
michael-denyer/signal-output-style
Signal: a Claude Code output style that answers first, sizes replies to the question, and makes every number carry its unit and source.
michael-denyer/terraform-lsp-cc-plugin
michael-denyer/marksman-lsp-cc-plugin
Marksman Markdown language server packaged as a Claude Code LSP plugin marketplace
michael-denyer/pyrefly-lsp-cc-plugin
Pyrefly LSP integration for Claude Code — fast Python type checking
michael-denyer/everything-must-go
michael-denyer/black-box-unlock
Code forensics and analysis tool - investigate your codebase like a crime scene