Repositories list

• phylostability

  Public
  Python

  •0•1•0•0•Updated Oct 1, 2024Oct 1, 2024

• larch

  Public
  Inference and manipulation of history DAGs

  C++

  •

  MIT License

  •2•2•14•2•Updated Sep 27, 2024Sep 27, 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•16•12•3•Updated Aug 27, 2024Aug 27, 2024

• transport

  Public
  Python

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

• multidms

  Public
  Joint modeling of multiple deep mutational scanning experiments

  Jupyter Notebook

  •

  MIT License

  •0•1•19•1•Updated Aug 13, 2024Aug 13, 2024

• sci-space-v2

  Public
  Jupyter Notebook

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

• dnsm-json-database

  Public
  Python

  •0•0•0•0•Updated Aug 6, 2024Aug 6, 2024

• phip-flow

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

  Python

  •

  MIT License

  •6•10•0•0•Updated Jul 22, 2024Jul 22, 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

• antigen

  Public
  Simulating virus evolution and epidemiology

  Mathematica

  •8•1•4•1•Updated Jul 2, 2024Jul 2, 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

• 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 Apr 16, 2024Apr 16, 2024

• seasonal-flu-dmsa

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

  Python

  •26•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•5•2•Updated Mar 1, 2024Mar 1, 2024

• SARS-CoV-2-S2-Abs

  Public
  Repository for Antibody Responses to SARS-CoV-2 S2 manuscript

  Jupyter Notebook

  •0•0•0•0•Updated Feb 28, 2024Feb 28, 2024

• phippery

  Public
  Python

  •

  MIT License

  •2•13•1•0•Updated Jan 23, 2024Jan 23, 2024

• hdag-benchmark

  Public
  Python

  •0•0•3•0•Updated Dec 11, 2023Dec 11, 2023

• infection-timing

  Public
  R

  •0•0•0•0•Updated Nov 7, 2023Nov 7, 2023

• usher

  Public
  Ultrafast Sample Placement on Existing Trees

  C++

  •

  MIT License

  •42•0•1•0•Updated Nov 3, 2023Nov 3, 2023

• CYP-multidms

  Public
  a repository for the analysis of C9 and C19 dms data

  Jupyter Notebook

  •0•0•0•1•Updated Oct 4, 2023Oct 4, 2023

• LK-SARS-CoV-2

  Public
  Repository for Linda Kizazi SARS-CoV-2 manuscript Analysis

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jun 28, 2023Jun 28, 2023

• zika-dmsa

  Public
  Nextstrain build for Zika virus with dms model phenotype predictions

  Python

  •10•0•0•0•Updated Apr 18, 2023Apr 18, 2023