Open-source research software from my PhD, plus a few general-purpose tools.
Simulation suite for adaptive immune receptor sequences
Generates immunoglobulin and T-cell receptor sequences with full ground-truth annotations, covering V(D)J recombination, somatic hypermutation, indels and sequencing corruption. C backend, 100+ built-in configurations across 23 species.
pip install GenAIRRDeep-learning aligner for immunoglobulin sequences
Multi-task neural network for allele assignment, segmentation and productivity calls with calibrated likelihoods. Available as a Python package, a container image and a web application.
pip install AlignAIRGraph models of immune repertoires
Generation probability, diversity and simulation for TCR and BCR repertoires from graph models of decomposed receptor sequences. Includes the FlashbackGraph implementation. Python with C acceleration.
pip install LZGraphsPython client for NCBI data retrieval
A small library for exploring and downloading records from NCBI databases.
Plotting functions for biomedical data
Figure helpers for common biomedical analyses, with consistent styling for papers and reports.
Remote progress monitoring for long-running jobs
Wraps any command and streams its progress to a browser over peer-to-peer WebRTC. Written in Go, with Homebrew and Scoop packages.
Reference code for "On bi-gram graph attributes" (2021)
Implementation of the algorithms and metrics described in the paper.