Research packages that other groups can install and run, and a few smaller 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. Rust simulation kernel behind a Python API, 106 built-in configurations across 23 species, and pre-built wheels for Linux, macOS and Windows.
$pip install GenAIRR
Deep-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 AlignAIR
Graph 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 LZGraphs
A small library for exploring and downloading records from NCBI databases.
Figure helpers for common biomedical analyses, with consistent styling for papers and reports.
Wraps any command and streams its progress to a browser over peer-to-peer WebRTC. Written in Go, with Homebrew and Scoop packages.
Implementation of the algorithms and metrics described in the paper.