Deep generative model of genetic variation data based on Probabilistic Circuits

Mathematical Programming in JAX

UCE is a zero-shot foundation model for single-cell gene expression data

Repository for edgePython which is a Python implementation of the Bioconductor edgeR package for differential analysis of genomics count data.

scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.

Analyze Massively Parallel Reporter Assay (MPRA) Data

Lightweight coding agent that runs in your terminal

Use as many MCP servers as you want while minimizing context usage. A code mode MCP server gateway driven with Lua 🌙

Efficient Differentiable n-d PDE Solvers in JAX.

Notes on the statistics background for statistical genetics trainees

Orthogonal polynomials with JAX

Gene Environment Interaction Estimator

A curated list of practical Codex skills for automating workflows across the Codex CLI and API.

An agentic skills framework & software development methodology that works.

Ed's repo of Claude Code plugins, centered around a research-plan-implement workflow. Only a tiny bit cursed. If you're lucky.

Tweaks for `mkdocstrings[python]`

JAXMg: A multi-GPU linear solver in JAX

Structural Time Series in JAX

SParse lINear solvers in JAX

The computational and statistical analyses of TenK10K phase 1 multiome data

A library for easy, fast, and efficient reading & writing of PLINK Bed files

A fast and flexible Python package for efficiently solving lasso, elastic net, group lasso, and group elastic net problems.

Simulation of exact paths for the Wright-Fisher diffusion and diffusion-bridge

CLI interfaces & config objects, from types

Code for implementing central flows

Manopt, a Matlab toolbox for optimization on manifolds

Intuitive, easy CLIs based on python type hints.