Repositories list

• netam

  Public
  Neural networks to model BCR affinity maturation

  Python

  •0•1•6•1•Updated Feb 12, 2025Feb 12, 2025

• phylostability

  Public
  Python

  •0•1•0•0•Updated Feb 11, 2025Feb 11, 2025

• larch

  Public
  Inference and manipulation of history DAGs

  C++

  •

  MIT License

  •2•2•14•2•Updated Feb 11, 2025Feb 11, 2025

• thrifty-experiments-1

  Public
  Jupyter Notebook

  •0•1•1•1•Updated Feb 10, 2025Feb 10, 2025

• phip-flow

  Public
  A Nextflow pipeline to align, merge, and organize large PhIP-Seq datasets

  Python

  •

  MIT License

  •6•11•0•0•Updated Feb 7, 2025Feb 7, 2025

• antigen

  Public
  Simulating virus evolution and epidemiology

  Mathematica

  •8•1•2•0•Updated Jan 30, 2025Jan 30, 2025

• ncov-ab-escape

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jan 22, 2025Jan 22, 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

• dasm-json-database-1

  Public
  Database of dms-viz jsons for DASM model (human only).

  0•0•0•0•Updated Jan 17, 2025Jan 17, 2025

• dnsm-json-database

  Public
  Python

  •0•0•0•0•Updated Jan 16, 2025Jan 16, 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 Jan 7, 2025Jan 7, 2025

• multidms

  Public
  Joint modeling of multiple deep mutational scanning experiments

  Jupyter Notebook

  •

  MIT License

  •0•1•21•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•14•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

• tex-template

  Public template
  TeX

  •0•2•1•0•Updated Sep 17, 2024Sep 17, 2024

• python-package-template

  Public template
  A template python package, put together by Jared and Dave

  MIT License

  •0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

• gctree

  Public
  GCtree: phylogenetic inference of genotype-collapsed trees

  phylogeneticssingle-cell

  Python

  •

  GNU General Public License v3.0

  •2•17•12•3•Updated Aug 27, 2024Aug 27, 2024

• transport

  Public
  Python

  •0•2•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

• SARS-CoV-2_spike_multidms

  Public
  Comparing DMS datasets for spike from Delta, Omicron BA.1, and Omicron BA.2

  Jupyter Notebook

  •0•1•0•0•Updated Jul 12, 2024Jul 12, 2024

• sdag-nni-experiments

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Jun 11, 2024Jun 11, 2024

• historydag

  Public
  Python

  •

  GNU General Public License v3.0

  •1•0•12•0•Updated May 16, 2024May 16, 2024

• LASV-manuscript-nextstrain-dmsa

  Public
  This repository holds the build code for generating a nextstrain tree with escape score predictions.

  Python

  •0•0•0•0•Updated Apr 23, 2024Apr 23, 2024

• lassa-dmsa

  Public
  Nextstrain build for Lassa virus

  Python

  •5•0•0•0•Updated Apr 22, 2024Apr 22, 2024

• seasonal-flu-dmsa

  Public
  Fork of seasonal-flu nextstrain build to include phenotype predictions informed by dms data.

  Python

  •27•0•0•0•Updated Mar 31, 2024Mar 31, 2024

• linearham

  Public
  A Bayesian Phylo-HMM for B cell receptor sequence analysis

  phylogeneticsimmunologyb-cell

  C++

  •4•6•6•2•Updated Mar 1, 2024Mar 1, 2024