Predictive kmer models for development use

A talking LLM that runs on your own computer without needing the internet.

direct RNA nanopore sequencing barcode design and demultiplexing

Explore 5,000+ genomes in the terminal. Light, blazing fast 🚀, vim-motion.

Rust implementation of Needleman-Wunsch & Smith-Waterman sequence alignment

Single-Cell Omics for Transcriptome CHaracterization (SCOTCH): isoform-level characterization of gene expression through long-read single-cell RNA sequencing

Simulator of an ONT device with ReadUntil gRPC support

Python wrapping multithreaded bindings to minimap2

CLI tool for flexible and fast adaptive sampling on ONT sequencers

A minimap2 implementation with binseq inputs

Like pigz, but rust

Single-cell epigenomics analysis tools

A reactive notebook for Python — run reproducible experiments, query with SQL, execute as a script, deploy as an app, and version with git. All in a modern, AI-native editor.

Rust bindings to minimap2 library

Python quantitative trading strategies including VIX Calculator, Pattern Recognition, Commodity Trading Advisor, Monte Carlo, Options Straddle, Shooting Star, London Breakout, Heikin-Ashi, Pair Tra…

A generative world for general-purpose robotics & embodied AI learning.

GEEES: Inferring Cell-specific Gene-Enhancer Interactions from Multi-modal Single Cell Data

Oxford Nanopore's Basecaller

Handout for a talk I gave about LLM and CLI tools

A library of free open source icons for science illustrations in biology and chemistry

Plain text project planning in Obsidian

TISSUE (Transcript Imputation with Spatial Single-cell Uncertainty Estimation) provides tools for estimating well-calibrated uncertainty measures for gene expression predictions in single-cell spat…

Amtrak fare-scraping service

Scaling Single Cell Analysis to Millions of Cells

Specification for the extended fragment geometry description language

Generate high quality, publication ready visualizations for single cell transcriptomics data.