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    • Code and data for: "Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences".
      R
      0000Updated Oct 30, 2024Oct 30, 2024
    • blotter

      Public
      bedford lab research
      HTML
      926721Updated Oct 28, 2024Oct 28, 2024
    • Mathematica
      44631Updated Oct 25, 2024Oct 25, 2024
    • Nextstrain build for SARS-CoV-2 to calculate immune escape of circulating viruses
      Mathematica
      MIT License
      403041Updated Oct 24, 2024Oct 24, 2024
    • Phylogenetic analysis and visualization of H1N1pdm neutralization data from Loes et al. 2024
      Python
      MIT License
      0000Updated Oct 16, 2024Oct 16, 2024
    • Jupyter Notebook
      0000Updated Oct 11, 2024Oct 11, 2024
    • R
      0100Updated Oct 10, 2024Oct 10, 2024
    • Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
      HTML
      MIT License
      1520Updated Oct 8, 2024Oct 8, 2024
    • Comparing fitness dynamics across SARS-CoV-2, influenza H3 and influenza H1
      Mathematica
      0100Updated Oct 5, 2024Oct 5, 2024
    • Timely vaccine strain selection and genomic surveillance improves evolutionary forecast accuracy of seasonal influenza A/H3N2
      Jupyter Notebook
      MIT License
      0020Updated Sep 29, 2024Sep 29, 2024
    • cholera

      Public
      Jupyter Notebook
      0100Updated Sep 27, 2024Sep 27, 2024
    • Seasonal flu build for analysis of antigenic evolution in ILI data
      Jupyter Notebook
      MIT License
      0000Updated Sep 5, 2024Sep 5, 2024
    • popcast

      Public
      Long-term forecasts for pathogen populations
      Python
      MIT License
      0100Updated Sep 4, 2024Sep 4, 2024
    • Assessing accuracy of fitness model forecasts
      Jupyter Notebook
      2160Updated Sep 2, 2024Sep 2, 2024
    • Create reduced dimension embeddings for pathogen sequences
      Python
      MIT License
      0160Updated Aug 21, 2024Aug 21, 2024
    • Script to build and deploy Bedford lab website
      Ruby
      0001Updated Aug 2, 2024Aug 2, 2024
    • An atlas of continuous adaptive evolution in endemic human viruses
      Jupyter Notebook
      0300Updated Aug 1, 2024Aug 1, 2024
    • analysis of updated MERS data via approximate structured coalescent approaches
      Jupyter Notebook
      0000Updated Jun 26, 2024Jun 26, 2024
    • vscode-guide

      Public template
      A guide on practical uses for the popular text editor by members of the Bedford Lab
      0000Updated Jun 18, 2024Jun 18, 2024
    • Correlating within-host and between-host fitness in SARS-CoV-2
      HTML
      0100Updated Jun 4, 2024Jun 4, 2024
    • evofr

      Public
      Tools for evolutionary forecasting
      Jupyter Notebook
      GNU Affero General Public License v3.0
      1431Updated Jun 3, 2024Jun 3, 2024
    • Phylodynamics of the 2022 mpox epidemic
      Jupyter Notebook
      4110Updated May 16, 2024May 16, 2024
    • ncov-orf8

      Public
      Positive selection for ORF8 knockout in SARS-CoV-2
      Jupyter Notebook
      MIT License
      0000Updated Mar 22, 2024Mar 22, 2024
    • Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
      Jupyter Notebook
      MIT License
      1500Updated Mar 20, 2024Mar 20, 2024
    • Analysis of predictive value of escape scores from Welsh et al. 2023 experimental data
      Python
      MIT License
      0000Updated Mar 13, 2024Mar 13, 2024
    • Manuscript and data describing joint visualization of influenza serology and phylogeny
      TeX
      MIT License
      0000Updated Mar 5, 2024Mar 5, 2024
    • Local-scale phylodynamics of SARS-CoV-2 in King County, WA
      Jupyter Notebook
      MIT License
      0010Updated Feb 20, 2024Feb 20, 2024
    • Nextstrain build to examine early outbreak of SARS-CoV-2 in Wuhan
      Python
      MIT License
      2201Updated Feb 17, 2024Feb 17, 2024
    • Code and data for "Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences"
      R
      1610Updated Feb 8, 2024Feb 8, 2024
    • veme-2022

      Public
      Workshop for VEME 2022: Real-time tracking of pathogen evolution using Nextstrain
      MIT License
      0400Updated Dec 5, 2023Dec 5, 2023