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    131 repositories

    • larch

      Public
      Inference and manipulation of history DAGs
      C++
      •
      MIT License
      •2•2•18•1•Updated Dec 19, 2025Dec 19, 2025

    • usher

      Public
      Ultrafast Sample Placement on Existing Trees
      C++
      •
      MIT License
      •47•0•1•0•Updated Dec 19, 2025Dec 19, 2025

    • olmsted

      Public
      B-cell repertoire and clonal family tree explorer
      JavaScript
      •
      GNU Affero General Public License v3.0
      •5•17•17•4•Updated Dec 17, 2025Dec 17, 2025

    • multidms

      Public
      Joint modeling of multiple deep mutational scanning experiments
      Jupyter Notebook
      •
      MIT License
      •0•1•19•1•Updated Dec 17, 2025Dec 17, 2025

    • 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
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•1•4•0•Updated Dec 15, 2025Dec 15, 2025

    • tex-template

      Public template
      TeX
      •0•3•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
      C++
      •4•6•5•2•Updated Dec 4, 2025Dec 4, 2025

    • netam

      Public
      Neural networks to model BCR affinity maturation
      Python
      •
      MIT License
      •2•5•8•0•Updated Dec 3, 2025Dec 3, 2025

    • fully-heterochronous-f-matrix

      Public
      F-matrix representation and sampling for ranked tree shapes
      R
      •0•0•0•0•Updated Nov 21, 2025Nov 21, 2025

    • gcdyn

      Public
      Inference of germinal center dynamics from replay data
      Jupyter Notebook
      •0•3•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
      0•4•0•0•Updated Oct 24, 2025Oct 24, 2025

    • 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 Oct 23, 2025Oct 23, 2025

    • ola-encoding

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

    • dasm-experiments

      Public
      Experiments and analysis code for the DASM manuscript
      Jupyter Notebook
      •0•0•0•0•Updated Oct 13, 2025Oct 13, 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

    • claude-code-agents

      Public
      Agents for Claude Code
      0•14•0•0•Updated Sep 29, 2025Sep 29, 2025

    • antigen

      Public
      Simulating virus evolution and epidemiology
      Mathematica
      •8•1•4•0•Updated Sep 26, 2025Sep 26, 2025

    • dnsm-models

      Public
      Deep natural selection models
      MIT License
      •0•0•0•0•Updated Sep 24, 2025Sep 24, 2025

    • thrifty-experiments-1

      Public
      Jupyter Notebook
      •
      MIT License
      •0•1•1•1•Updated Sep 18, 2025Sep 18, 2025

    • dnsm-experiments-mbe

      Public
      Deep Natural Selection Model (DNSM) experiments archive for MBE publication
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

    • preflight

      Public
      TeX
      •4•9•0•0•Updated Sep 16, 2025Sep 16, 2025

    • pdf-navigator-mcp

      Public
      Comprehensive MCP server for PDF reading, navigation, and text search
      Python
      •
      MIT License
      •0•6•0•0•Updated Sep 8, 2025Sep 8, 2025

    • larch-example-data

      Public
      0•0•0•0•Updated Jul 23, 2025Jul 23, 2025

    • hdag-benchmark

      Public
      Python
      •0•0•3•0•Updated Jul 10, 2025Jul 10, 2025

    • mcp-compute-scout

      Public
      MCP server for checking compute and GPU availability across multiple servers
      Python
      •0•1•0•0•Updated Jul 7, 2025Jul 7, 2025

    • dnsm-json-database

      Public
      Python
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025