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    122 repositories

    • olmsted

      Public
      B-cell repertoire and clonal family tree explorer
      JavaScript
      •
      GNU Affero General Public License v3.0
      •4•16•65•2•Updated Aug 8, 2025Aug 8, 2025

    • multidms

      Public
      Joint modeling of multiple deep mutational scanning experiments
      Jupyter Notebook
      •
      MIT License
      •0•1•20•2•Updated Aug 7, 2025Aug 7, 2025

    • netam

      Public
      Neural networks to model BCR affinity maturation
      Python
      •0•1•12•1•Updated Aug 7, 2025Aug 7, 2025

    • tex-template

      Public template
      TeX
      •0•2•1•0•Updated Aug 7, 2025Aug 7, 2025

    • antigen

      Public
      Simulating virus evolution and epidemiology
      Mathematica
      •8•1•4•1•Updated Aug 6, 2025Aug 6, 2025

    • ola-encoding

      Public
      Python
      •0•1•0•0•Updated Aug 5, 2025Aug 5, 2025

    • pdf-navigator-mcp

      Public
      Comprehensive MCP server for PDF reading, navigation, and text search
      Python
      •
      MIT License
      •0•4•0•0•Updated Aug 3, 2025Aug 3, 2025

    • usher

      Public
      Ultrafast Sample Placement on Existing Trees
      C++
      •
      MIT License
      •46•0•1•0•Updated Jul 31, 2025Jul 31, 2025

    • larch

      Public
      Inference and manipulation of history DAGs
      C++
      •
      MIT License
      •2•2•15•1•Updated Jul 23, 2025Jul 23, 2025

    • larch-example-data

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

    • dnsm-experiments-mbe

      Public
      Deep Natural Selection Model (DNSM) experiments archive for MBE publication
      Jupyter Notebook
      •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

    • hdag-benchmark

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

    • thrifty-experiments-1

      Public
      Jupyter Notebook
      •0•1•1•1•Updated Jul 10, 2025Jul 10, 2025

    • gcdyn

      Public
      Inference of germinal center dynamics from replay data
      Jupyter Notebook
      •0•0•22•1•Updated Jul 9, 2025Jul 9, 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

    • epam

      Public
      Evaluating predictions of affinity maturation
      Python
      •
      MIT License
      •0•1•0•0•Updated Jul 3, 2025Jul 3, 2025

    • dnsm-json-database

      Public
      Python
      •0•0•0•0•Updated Jun 10, 2025Jun 10, 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•3•0•Updated Jun 7, 2025Jun 7, 2025

    • gcreplay-viz

      Public
      Jupyter Notebook
      •0•0•0•0•Updated May 23, 2025May 23, 2025

    • dasm-json-database-1

      Public
      Database of dms-viz jsons for DASM model (human only).
      0•0•0•0•Updated Apr 13, 2025Apr 13, 2025

    • SARS2-synonymous-mut-rate

      Public
      Using mutation counts from UShER to estimate SARS-CoV-2's mutation rate
      Jupyter Notebook
      •0•1•0•0•Updated Apr 2, 2025Apr 2, 2025

    • python-package-template

      Public template
      A template python package, put together by Jared and Dave
      Python
      •1•1•7•0•Updated Mar 31, 2025Mar 31, 2025

    • phylostability

      Public
      Python
      •0•1•0•0•Updated Feb 13, 2025Feb 13, 2025

    • phip-flow

      Public
      A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets
      Python
      •
      MIT License
      •8•13•1•0•Updated Feb 7, 2025Feb 7, 2025

    • ncov-ab-escape

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • ncov-dmsa

      Public
      a fork of the ncov Nextflow pipeline with the addition of some materials to run polyclonal escape predictions.
      Python
      •
      MIT License
      •0•0•1•0•Updated Jan 17, 2025Jan 17, 2025

    • dmsa-pred

      Public
      A standalone package for using deep mutational scanning data to predict the phenotypes of untested sequences from a multiple-sequence alignment.
      Python
      •0•0•1•0•Updated Jan 17, 2025Jan 17, 2025

    • thrifty-models

      Public
      MIT License
      •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

    • phippery

      Public
      Python
      •
      MIT License
      •2•19•1•0•Updated Nov 7, 2024Nov 7, 2024

    • gctree2-validation-plots

      Public
      Python
      •0•0•0•0•Updated Sep 26, 2024Sep 26, 2024