UMAP, but accelerated.

Fast genomics quality control tools for sequencing data, written in Rust.

The agent harness performance optimization system. Skills, instincts, memory, security, and research-first development for Claude Code, Codex, Opencode, Cursor and beyond.

Interactive Pytorch forward pass visualization in notebooks

Permutect, an incredibly efficient deep learning architecture for somatic and germline variant calling

Introduction to Computational Biology and Bioinformatics Course at Caltech, 2026

🔗 Source code of my homepage build with {blogdown}, HUGO and Netlify

PyComplexHeatmap: A Python package to plot complex heatmap (clustermap)

A unified framework for machine learning with time series

An efficient CLI to extract sequences from the SRA

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

CAncer Standards Long-read Evaluation

A modern resume template written in Typst, inspired by Awesome-CV

best way to save what you love

Tidy Plots for Scientific Papers

Download sequencing data and metadata from GSA, SRA, ENA, and DDBJ databases.

Visualizer for neural network, deep learning and machine learning models

Genomics Extension for SQLite

A Snakemake pipeline developed to quantify isoforms expression levels in large RNA-seq datasets and find poly-A sites

Publication-quality network visualisations in python

A Wes Anderson color palette for R

A visualization grammar and GPU-accelerated toolkit for genomic data

Benchmarks for classification of genomic sequences

aka "Bayesian Methods for Hackers": An introduction to Bayesian methods + probabilistic programming with a computation/understanding-first, mathematics-second point of view. All in pure Python ;)

[Python] Comparison of empirical probability distributions. Integral probability metrics (e.g. Kantorovich metric). f-divergences (e.g. Kullback-Leibler). Application to the Choquet integral.

Interactive lessons in bioinformatics.