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@flu-crew Flu-crew at the National Animal Disease Center

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    29 repositories

    • TreeSort

      Public
      Virus reassortment inference software. Infers both recent and ancestral reassortment and uses flexible molecular clock constraints.
      Python
      •
      MIT License
      •0•8•0•0•Updated Nov 29, 2024Nov 29, 2024

    • dairy-cattle-hpai-experiment

      Public
      data and code to support Baker et al. HPAI H5N1 in dairy cattle
      MIT License
      •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • phylo-rs

      Public
      Library for phylogenetic trees
      Rust
      •
      MIT License
      •3•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • octoflushow

      Public
      A Shiny app for swine IAV surveillance
      R
      •
      MIT License
      •1•2•6•0•Updated Oct 25, 2024Oct 25, 2024

    • octofludb

      Public
      A local flu knowledgebase
      Python
      •0•0•2•1•Updated Oct 24, 2024Oct 24, 2024

    • parnas

      Public
      Phylogenetic maximum representation sampling: choosing most representative strains or taxa
      Python
      •
      MIT License
      •2•29•1•0•Updated Oct 17, 2024Oct 17, 2024

    • Flumina

      Public
      A pipeline for the analysis of Illumina sequence data from Influenza viruses
      R
      •
      GNU General Public License v3.0
      •1•3•0•0•Updated Aug 29, 2024Aug 29, 2024

    • classLog

      Public
      Zeller et al. Logistic regression classifier for genetic sequences
      Python
      •
      GNU General Public License v2.0
      •1•3•0•0•Updated Jul 29, 2024Jul 29, 2024

    • datasets

      Public
      flu-crew datasets used in manuscripts, tutorials, and other work.
      R
      •
      MIT License
      •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

    • dairy-cattle-hpai-2024

      Public
      code to reproduce analysis in Nguyen et al.
      R
      •
      MIT License
      •0•2•0•0•Updated Jul 17, 2024Jul 17, 2024

    • octoFLU

      Public
      Script that labels phylogenetic clades based on the clade of the nearest neighbor using patristic distances determined from the tree.
      Python
      •7•9•1•1•Updated Feb 7, 2024Feb 7, 2024

    • FluPore

      Public
      supporting the publication of and education about the software PURDY
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Feb 6, 2024Feb 6, 2024

    • histology_segmentation

      Public
      SmartHisto is a Deep Bayesian Neural Network Framework that can annotate and identify classes in histology sections
      Python
      •
      MIT License
      •1•0•0•0•Updated Dec 19, 2023Dec 19, 2023

    • gallimaufry

      Public
      A collection of useful scripts
      Python
      •
      MIT License
      •0•0•0•0•Updated Nov 22, 2023Nov 22, 2023

    • FairProportion_Index

      Public
      A tool to compute the FP Index
      Python
      •1•0•0•0•Updated Nov 17, 2023Nov 17, 2023

    • pdm-spillovers

      Public
      Analysis of the H1N1pdm09 influenza A lineage and associated interspecies spillovers (2009-2021) between humans and swine in the US
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 12, 2023Oct 12, 2023

    • h3-iva-evolution

      Public
      Code and data associated with Neveau et al H3-IVa evolution manuscript
      R
      •0•0•0•0•Updated Jul 27, 2023Jul 27, 2023

    • PD_stats

      Public
      A project designed with algorithms to compute PD Stats
      Python
      •2•5•0•0•Updated Jul 26, 2023Jul 26, 2023

    • seq_class

      Public
      Rust
      •
      MIT License
      •1•0•0•0•Updated Apr 14, 2023Apr 14, 2023

    • N1-diversity

      Public
      N1 evolution and genetic and antigenic diversity
      R
      •0•0•0•0•Updated Feb 3, 2023Feb 3, 2023

    • flutile

      Public
      flu utilities
      Python
      •
      MIT License
      •0•9•2•0•Updated Feb 1, 2023Feb 1, 2023

    • smot

      Public
      Simple Manipulation Of Trees
      Python
      •
      MIT License
      •4•13•0•0•Updated Dec 20, 2022Dec 20, 2022

    • h1-risk-pipeline

      Public
      Analysis and files for Venkatesh et al. (swine IAV H1 zoonotic risk)
      HTML
      •
      MIT License
      •1•0•0•0•Updated Sep 13, 2022Sep 13, 2022

    • rf-net-2

      Public
      Phylogenetic network inference for reassortment detection using rf-net-2
      MIT License
      •1•6•0•0•Updated Jun 30, 2022Jun 30, 2022

    • h3-risk-pipeline

      Public
      Analysis and files for Souza et al. (swine IAV H3 zoonotic risk)
      R
      •
      MIT License
      •0•0•0•0•Updated May 9, 2022May 9, 2022

    • n2-diversity

      Public
      Analysis files and graphics for Zeller et al. (swine IAV N2.2002 neuraminidase from 2009-2018)
      R
      •
      MIT License
      •0•1•1•0•Updated Sep 14, 2021Sep 14, 2021

    • docs

      Public
      Documentation, examples, tutorials and such
      HTML
      •0•0•1•0•Updated Apr 14, 2021Apr 14, 2021

    • n2-characterization

      Public
      phylogenetic analyses from Kaplan et al N2 characterization manuscript
      MIT License
      •0•0•1•0•Updated Apr 9, 2021Apr 9, 2021

    • antigenic-prediction

      Public
      Code for Zeller et al. machine learning prediction of antigenic drift in swine IAV
      Python
      •
      MIT License
      •3•1•0•0•Updated Mar 18, 2021Mar 18, 2021