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    • netam

      Public
      Neural networks to model BCR affinity maturation
      Python
      0160Updated Nov 16, 2024Nov 16, 2024
    • Python
      0000Updated Nov 14, 2024Nov 14, 2024
    • larch

      Public
      Inference and manipulation of history DAGs
      C++
      MIT License
      22142Updated Nov 14, 2024Nov 14, 2024
    • MIT License
      0000Updated Nov 13, 2024Nov 13, 2024
    • phip-flow

      Public
      A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets
      Python
      MIT License
      61100Updated Nov 7, 2024Nov 7, 2024
    • phippery

      Public
      Python
      MIT License
      21400Updated Nov 7, 2024Nov 7, 2024
    • usher

      Public
      Ultrafast Sample Placement on Existing Trees
      C++
      MIT License
      42010Updated Oct 24, 2024Oct 24, 2024
    • Python
      0100Updated Oct 1, 2024Oct 1, 2024
    • Python
      0000Updated Sep 26, 2024Sep 26, 2024
    • Jupyter Notebook
      GNU General Public License v3.0
      8331Updated Sep 20, 2024Sep 20, 2024
    • tex-template

      Public template
      TeX
      0210Updated Sep 17, 2024Sep 17, 2024
    • A template python package, put together by Jared and Dave
      MIT License
      0000Updated Sep 11, 2024Sep 11, 2024
    • gctree

      Public
      GCtree: phylogenetic inference of genotype-collapsed trees
      Python
      GNU General Public License v3.0
      216123Updated Aug 27, 2024Aug 27, 2024
    • transport

      Public
      Python
      0212Updated Aug 24, 2024Aug 24, 2024
    • multidms

      Public
      Joint modeling of multiple deep mutational scanning experiments
      Jupyter Notebook
      MIT License
      01191Updated Aug 13, 2024Aug 13, 2024
    • Jupyter Notebook
      0210Updated Aug 6, 2024Aug 6, 2024
    • phip-viz

      Public
      Python
      03110Updated Jul 16, 2024Jul 16, 2024
    • Comparing DMS datasets for spike from Delta, Omicron BA.1, and Omicron BA.2
      Jupyter Notebook
      0100Updated Jul 12, 2024Jul 12, 2024
    • antigen

      Public
      Simulating virus evolution and epidemiology
      Mathematica
      8141Updated Jul 2, 2024Jul 2, 2024
    • Jupyter Notebook
      0000Updated Jun 11, 2024Jun 11, 2024
    • Python
      GNU General Public License v3.0
      10120Updated May 16, 2024May 16, 2024
    • This repository holds the build code for generating a nextstrain tree with escape score predictions.
      Python
      0000Updated Apr 23, 2024Apr 23, 2024
    • Nextstrain build for Lassa virus
      Python
      5000Updated Apr 22, 2024Apr 22, 2024
    • 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
      0010Updated Apr 16, 2024Apr 16, 2024
    • Fork of seasonal-flu nextstrain build to include phenotype predictions informed by dms data.
      Python
      26000Updated Mar 31, 2024Mar 31, 2024
    • linearham

      Public
      A Bayesian Phylo-HMM for B cell receptor sequence analysis
      C++
      4652Updated Mar 1, 2024Mar 1, 2024
    • Repository for Antibody Responses to SARS-CoV-2 S2 manuscript
      Jupyter Notebook
      0000Updated Feb 28, 2024Feb 28, 2024
    • Python
      0030Updated Dec 11, 2023Dec 11, 2023
    • R
      0000Updated Nov 7, 2023Nov 7, 2023
    • a repository for the analysis of C9 and C19 dms data
      Jupyter Notebook
      0001Updated Oct 4, 2023Oct 4, 2023