Skip to content

@matsengrp Matsen Group

Change the repository type filter

All

    Repositories list

    136 repositories

    • multidms

      Public
      Joint modeling of multiple deep mutational scanning experiments
      Python
      •
      MIT License
      •0•2•15•0•Updated Apr 4, 2026Apr 4, 2026

    • olmsted

      Public
      B-cell repertoire and clonal family tree explorer
      JavaScript
      •
      GNU Affero General Public License v3.0
      •6•18•13•5•Updated Apr 3, 2026Apr 3, 2026

    • larch2

      Public
      C++
      •
      MIT License
      •0•0•5•1•Updated Apr 2, 2026Apr 2, 2026

    • SARS-CoV-2_spike_multidms

      Public
      Comparing DMS datasets for spike from Delta, Omicron BA.1, and Omicron BA.2
      Jupyter Notebook
      •0•1•1•0•Updated Mar 30, 2026Mar 30, 2026

    • larch

      Public
      Inference and manipulation of history DAGs
      C++
      •
      MIT License
      •2•2•19•4•Updated Mar 26, 2026Mar 26, 2026

    • dasm-experiments

      Public
      Experiments and analysis code for the DASM manuscript
      Jupyter Notebook
      •
      MIT License
      •0•0•2•2•Updated Mar 24, 2026Mar 24, 2026

    • flu-usher

      Public
      Jupyter Notebook
      •0•0•4•0•Updated Mar 20, 2026Mar 20, 2026

    • flu-mut-rates

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 19, 2026Mar 19, 2026

    • historydag

      Public
      Python
      •
      GNU General Public License v3.0
      •1•0•13•0•Updated Mar 16, 2026Mar 16, 2026

    • partis-zig-core

      Public
      Zig
      •0•0•1•0•Updated Mar 12, 2026Mar 12, 2026

    • gcreplay

      Public
      This repository contains the code and data for the analysis of B cell receptor (BCR) sequences isolated in Germinal Center (GC) - Replay experiments.
      replaycentergerminal
      replaycentergerminal
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•4•0•Updated Mar 2, 2026Mar 2, 2026

    • dnsm-experiments-mbe

      Public
      Deep Natural Selection Model (DNSM) experiments archive for MBE publication
      Jupyter Notebook
      •
      MIT License
      •1•0•0•0•Updated Feb 25, 2026Feb 25, 2026

    • fully-heterochronous-f-matrix

      Public
      F-matrix representation and sampling for ranked tree shapes
      R
      •0•0•0•0•Updated Feb 19, 2026Feb 19, 2026

    • partis

      Public
      B- and T-cell receptor sequence annotation, simulation, clonal family, and germline inference
      Python
      •
      GNU General Public License v3.0
      •33•0•0•0•Updated Feb 13, 2026Feb 13, 2026

    • claude-code-agents

      Public
      Agents for Claude Code
      1•21•0•0•Updated Jan 30, 2026Jan 30, 2026

    • antigen-prime

      Public
      Simulating virus evolution and epidemiology
      Wolfram Language
      •8•1•4•0•Updated Jan 23, 2026Jan 23, 2026

    • antigen-forecasting

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•4•2•Updated Jan 23, 2026Jan 23, 2026

    • usher

      Public
      Ultrafast Sample Placement on Existing Trees
      C++
      •
      MIT License
      •47•0•1•0•Updated Jan 20, 2026Jan 20, 2026

    • SARS2-mut-fitness-v2

      Public
      Repository for computing fitness effects of nucletoide and amino acid mutations based on accurate neutral rates.
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Jan 14, 2026Jan 14, 2026

    • tex-template

      Public template
      TeX
      •0•4•1•0•Updated Dec 9, 2025Dec 9, 2025

    • ncov-ab-escape

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 8, 2025Dec 8, 2025

    • s2trajectory

      Public
      SARS2-mut-fitness-trajectory
      Jupyter Notebook
      •0•1•12•1•Updated Dec 8, 2025Dec 8, 2025

    • linearham

      Public
      A Bayesian Phylo-HMM for B cell receptor sequence analysis
      phylogeneticsimmunologyb-cell
      phylogeneticsimmunologyb-cell
      C++
      •4•6•5•2•Updated Dec 4, 2025Dec 4, 2025

    • netam

      Public
      Neural networks to model BCR affinity maturation
      Python
      •
      MIT License
      •2•11•8•0•Updated Dec 3, 2025Dec 3, 2025

    • gcdyn

      Public
      Inference of germinal center dynamics from replay data
      Jupyter Notebook
      •1•4•22•1•Updated Nov 19, 2025Nov 19, 2025

    • epam

      Public
      Evaluating predictions of affinity maturation
      Python
      •
      MIT License
      •0•2•0•0•Updated Oct 27, 2025Oct 27, 2025

    • plugins

      Public
      Claude Code plugin with specialized agents for scientific writing, code review, and technical documentation
      4•18•0•0•Updated Oct 24, 2025Oct 24, 2025

    • ola-encoding

      Public
      Python
      •0•1•0•0•Updated Oct 21, 2025Oct 21, 2025

    • dasm-models

      Public
      MIT License
      •0•0•0•0•Updated Oct 12, 2025Oct 12, 2025

    • ig-sw

      Public
      Smith-Waterman alignment for immunoglobulins
      C++
      •0•3•1•0•Updated Oct 1, 2025Oct 1, 2025
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.