Repositories list

• larch

  Public
  Inference and manipulation of history DAGs

  C++

  •

  MIT License

  •2•2•14•1•Updated Jun 10, 2025Jun 10, 2025

• dnsm-json-database

  Public
  Python

  •0•0•0•0•Updated Jun 10, 2025Jun 10, 2025

• netam

  Public
  Neural networks to model BCR affinity maturation

  Python

  •0•1•9•1•Updated Jun 9, 2025Jun 9, 2025

• gcdyn

  Public
  Inference of germinal center dynamics from replay data

  Jupyter Notebook

  •0•0•22•2•Updated Jun 8, 2025Jun 8, 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

• epam

  Public
  Evaluating predictions of affinity maturation

  Python

  •

  MIT License

  •0•0•0•0•Updated Jun 3, 2025Jun 3, 2025

• gcreplay-viz

  Public
  Jupyter Notebook

  •0•0•0•0•Updated May 23, 2025May 23, 2025

• hdag-benchmark

  Public
  Python

  •0•0•3•0•Updated May 16, 2025May 16, 2025

• thrifty-experiments-1

  Public
  Jupyter Notebook

  •0•1•1•1•Updated May 16, 2025May 16, 2025

• tex-template

  Public template
  TeX

  •0•2•1•0•Updated Apr 25, 2025Apr 25, 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

• antigen

  Public
  Simulating virus evolution and epidemiology

  Mathematica

  •8•1•2•0•Updated Apr 2, 2025Apr 2, 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

• ola-encoding

  Public
  Python

  •0•1•0•0•Updated Mar 19, 2025Mar 19, 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

  •7•12•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

• multidms

  Public
  Joint modeling of multiple deep mutational scanning experiments

  Jupyter Notebook

  •

  MIT License

  •0•2•20•2•Updated Dec 2, 2024Dec 2, 2024

• thrifty-models

  Public
  MIT License

  •0•0•0•0•Updated Nov 13, 2024Nov 13, 2024

• phippery

  Public
  Python

  •

  MIT License

  •2•18•1•0•Updated Nov 7, 2024Nov 7, 2024

• usher

  Public
  Ultrafast Sample Placement on Existing Trees

  C++

  •

  MIT License

  •42•0•1•0•Updated Oct 24, 2024Oct 24, 2024

• gctree2-validation-plots

  Public
  Python

  •0•0•0•0•Updated Sep 26, 2024Sep 26, 2024

• bcr-phylo-benchmark

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •8•3•3•1•Updated Sep 20, 2024Sep 20, 2024

• gctree

  Public
  GCtree: phylogenetic inference of genotype-collapsed trees

  phylogeneticssingle-cell

  Python

  •

  GNU General Public License v3.0

  •2•18•13•3•Updated Aug 27, 2024Aug 27, 2024

• transport

  Public
  Python

  •0•3•1•2•Updated Aug 24, 2024Aug 24, 2024

• sci-space-v2

  Public
  Jupyter Notebook

  •0•2•1•0•Updated Aug 6, 2024Aug 6, 2024

• phip-viz

  Public
  Python

  •0•3•11•0•Updated Jul 16, 2024Jul 16, 2024