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    103 repositories

    • blotter

      Public
      bedford lab research
      HTML
      •93•67•2•2•Updated Nov 20, 2024Nov 20, 2024

    • rt-from-frequency-dynamics

      Public
      Inferring variant-specific effective reproduction numbers from combined case and sequencing data
      Mathematica
      •4•46•3•1•Updated Nov 20, 2024Nov 20, 2024

    • phylo-kernel-public

      Public
      Code and data for: "Fine-scale spatial and social patterns of SARS-CoV-2 transmission from identical pathogen sequences".
      R
      •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • relative-fitness-mechanisms

      Public
      Frequency dynamics predict viral fitness, antigenic relationships and epidemic growth
      Jupyter Notebook
      •0•1•0•0•Updated Nov 16, 2024Nov 16, 2024

    • fitness-flux

      Public
      Fitness dynamics of SARS-CoV-2 and seasonal influenza H3N2
      Mathematica
      •1•1•0•0•Updated Nov 12, 2024Nov 12, 2024

    • loes-2024-neutralization-nextstrain

      Public
      Phylogenetic analysis and visualization of H1N1pdm neutralization data from Loes et al. 2024
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • evofr

      Public
      Tools for evolutionary forecasting
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •1•4•3•0•Updated Nov 8, 2024Nov 8, 2024

    • ncov-escape

      Public
      Nextstrain build for SARS-CoV-2 to calculate immune escape of circulating viruses
      Mathematica
      •
      MIT License
      •403•0•4•1•Updated Nov 7, 2024Nov 7, 2024

    • mers-evolution

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

    • ncov-usa-mig

      Public
      R
      •0•1•0•0•Updated Oct 10, 2024Oct 10, 2024

    • cartography

      Public
      Dimensionality reduction distills complex evolutionary relationships in seasonal influenza and SARS-CoV-2
      HTML
      •
      MIT License
      •1•5•2•0•Updated Oct 8, 2024Oct 8, 2024

    • flu-forecasting-delays

      Public
      Timely vaccine strain selection and genomic surveillance improves evolutionary forecast accuracy of seasonal influenza A/H3N2
      Jupyter Notebook
      •
      MIT License
      •0•0•2•0•Updated Sep 29, 2024Sep 29, 2024

    • cholera

      Public
      Jupyter Notebook
      •0•1•0•0•Updated Sep 27, 2024Sep 27, 2024

    • perofsky-ili-antigenicity

      Public
      Seasonal flu build for analysis of antigenic evolution in ILI data
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 5, 2024Sep 5, 2024

    • popcast

      Public
      Long-term forecasts for pathogen populations
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 4, 2024Sep 4, 2024

    • ncov-forecasting-fit

      Public
      Assessing accuracy of fitness model forecasts
      Jupyter Notebook
      •2•1•6•0•Updated Sep 2, 2024Sep 2, 2024

    • pathogen-embed

      Public
      Create reduced dimension embeddings for pathogen sequences
      Python
      •
      MIT License
      •0•1•6•0•Updated Aug 21, 2024Aug 21, 2024

    • blotter-deploy

      Public
      Script to build and deploy Bedford lab website
      Ruby
      •0•0•0•1•Updated Aug 2, 2024Aug 2, 2024

    • adaptive-evolution

      Public
      An atlas of continuous adaptive evolution in endemic human viruses
      Jupyter Notebook
      •0•3•0•0•Updated Aug 1, 2024Aug 1, 2024

    • mers_skyline

      Public
      analysis of updated MERS data via approximate structured coalescent approaches
      Jupyter Notebook
      •0•0•0•0•Updated 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
      0•0•0•0•Updated Jun 18, 2024Jun 18, 2024

    • sars2-within-host-selection

      Public
      Correlating within-host and between-host fitness in SARS-CoV-2
      HTML
      •0•1•0•0•Updated Jun 4, 2024Jun 4, 2024

    • mpox-dynamics

      Public
      Phylodynamics of the 2022 mpox epidemic
      Jupyter Notebook
      •4•1•1•0•Updated May 16, 2024May 16, 2024

    • ncov-orf8

      Public
      Positive selection for ORF8 knockout in SARS-CoV-2
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Mar 22, 2024Mar 22, 2024

    • flu-forecasting

      Public
      Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution
      modelingpredictioninfluenza
      Jupyter Notebook
      •
      MIT License
      •1•5•0•0•Updated Mar 20, 2024Mar 20, 2024

    • welsh-escape-scores

      Public
      Analysis of predictive value of escape scores from Welsh et al. 2023 experimental data
      Python
      •
      MIT License
      •0•0•0•0•Updated Mar 13, 2024Mar 13, 2024

    • measurements-panel

      Public
      Manuscript and data describing joint visualization of influenza serology and phylogeny
      TeX
      •
      MIT License
      •0•0•0•0•Updated Mar 5, 2024Mar 5, 2024

    • ncov-king-county

      Public
      Local-scale phylodynamics of SARS-CoV-2 in King County, WA
      Jupyter Notebook
      •
      MIT License
      •0•0•1•0•Updated Feb 20, 2024Feb 20, 2024

    • ncov-early-outbreak

      Public
      Nextstrain build to examine early outbreak of SARS-CoV-2 in Wuhan
      Python
      •
      MIT License
      •2•2•0•1•Updated Feb 17, 2024Feb 17, 2024

    • size-genetic-clusters

      Public
      Code and data for "Estimating the reproduction number and transmission heterogeneity from the size distribution of clusters of identical pathogen sequences"
      R
      •1•6•1•0•Updated Feb 8, 2024Feb 8, 2024