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    35 repositories

    • outbreak.info

      Public
      During outbreaks of emerging diseases such as COVID-19, efficiently collecting, sharing, and integrating data is critical to scientific research. outbreak.info is a resource to aggregate all this information into a single location.
      outbreaksemerging-diseases
      Vue
      •
      GNU General Public License v3.0
      •13•33•212•5•Updated Nov 1, 2024Nov 1, 2024

    • wastewater

      Public
      Parser to incorporate to query lineage wastewater
      Python
      •0•1•0•1•Updated Oct 25, 2024Oct 25, 2024

    • python-outbreak-info

      Public
      Python package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info
      genomicsvariantsgenomics-visualizationgenomics-datacovid-19sars-cov-2covid-data
      Jupyter Notebook
      •
      MIT License
      •2•6•0•2•Updated Oct 1, 2024Oct 1, 2024

    • outbreak.api

      Public
      The data API server for outbreak.info
      Python
      •
      Apache License 2.0
      •9•11•46•11•Updated Jun 3, 2024Jun 3, 2024

    • genomics_api

      Public
      Python
      •0•0•0•0•Updated Dec 4, 2023Dec 4, 2023

    • outbreak-reporter

      Public
      Python
      •2•0•0•0•Updated Nov 6, 2023Nov 6, 2023

    • significance

      Public
      Python
      •0•0•0•0•Updated Oct 18, 2023Oct 18, 2023

    • growth_rate

      Public
      Python
      •0•0•0•0•Updated Sep 26, 2023Sep 26, 2023

    • covid19_LST_reports

      Public
      Python
      •3•0•0•0•Updated Jul 20, 2023Jul 20, 2023

    • protocolsio

      Public
      COVID-19 related Protocol metadata from Protocols.io
      Python
      •1•0•0•1•Updated Jul 20, 2023Jul 20, 2023

    • litcovid

      Public
      parser for LitCOVID Publications
      Python
      •3•1•9•0•Updated Jul 20, 2023Jul 20, 2023

    • dataverses

      Public
      Python
      •0•0•0•1•Updated Jul 20, 2023Jul 20, 2023

    • covid_who_clinical_trials

      Public
      Parser to incorporate COVID-19 clinical trial data from the WHO International Clinical Trials Registry Platform
      Python
      •
      MIT License
      •1•0•0•0•Updated Jul 20, 2023Jul 20, 2023

    • covid_pdb_datasets

      Public
      Parser to upload SARS-CoV-2 and COVID-19-related protein strutures
      Python
      •
      MIT License
      •1•0•1•0•Updated Jul 20, 2023Jul 20, 2023

    • covid_imperial_college

      Public
      outbreak.info meta data parser for Imperial College London resources
      Jupyter Notebook
      •1•0•0•0•Updated Jul 20, 2023Jul 20, 2023

    • covid_figshare

      Public
      Parser to upload COVID-19-related Figshare entries and standardize to schema.org/outbreak.info schema
      Python
      •
      MIT License
      •2•0•0•0•Updated Jul 20, 2023Jul 20, 2023

    • clinical_trials

      Public
      Parser to import COVID-19 clinical trials from clinicaltrials.gov
      Python
      •
      MIT License
      •1•0•1•1•Updated Jul 20, 2023Jul 20, 2023

    • biorxiv

      Public
      data plugin for covid related publications from biorvix
      Python
      •3•0•1•0•Updated Jul 20, 2023Jul 20, 2023

    • biothings_covid19

      Public
      Biothings plugin for JHU CSSE COVID-19 cases
      Python
      •5•6•10•4•Updated Jul 20, 2023Jul 20, 2023

    • .github

      Public
      0•0•0•0•Updated May 9, 2023May 9, 2023

    • R-outbreak-info

      Public
      R package to access the genomics and epidemiology data and Research Library metadata compiled and standardized on outbreak.info.
      genomicsrstatsepidemiologygenomics-visualizationgenomics-datarstats-package
      R
      •
      MIT License
      •10•20•32•1•Updated Mar 5, 2023Mar 5, 2023

    • outbreak_preprint_matcher

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • outbreak_parser_tools

      Public
      Python
      •
      Creative Commons Zero v1.0 Universal
      •1•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • topic_classifier

      Public
      Python
      •2•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • outbreak.info-resources

      Public template
      A curated repository of metadata of resources on COVID-19 and SARS-CoV-2
      Python
      •
      MIT License
      •4•0•54•1•Updated Dec 15, 2022Dec 15, 2022

    • outbreak-resources-paper

      Public
      Figures and data for the outbreak.info resources paper
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • covid_altmetrics

      Public
      Jupyter Notebook
      •1•2•0•0•Updated Dec 15, 2022Dec 15, 2022

    • covid19_LST_report_data

      Public
      repository for parsed covid19LST reports
      1•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • covid19_LST_annotations

      Public
      Python
      •0•0•0•0•Updated Dec 15, 2022Dec 15, 2022

    • outbreak-network

      Public
      outbreak.network list
      HTML
      •0•0•0•0•Updated Apr 13, 2022Apr 13, 2022