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    30 repositories

    • rase-pipeline

      Public
      RASE pipeline for inferring antibiotic resistance and susceptibility using genomic neighbor typing.
      Python
      •
      MIT License
      •1•6•5•0•Updated Nov 26, 2024Nov 26, 2024

    • Focusing-a-Viral-Risk-Ranking-Tool-on-Prediction

      Public
      R
      •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

    • Spillover-Evaluation

      Public
      R
      •0•0•0•0•Updated Sep 7, 2024Sep 7, 2024

    • LAC_testing

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated Jun 28, 2023Jun 28, 2023

    • FungalPathogens

      Public
      MIT License
      •0•0•0•0•Updated Jun 22, 2023Jun 22, 2023

    • cov19flightimport

      Public
      Data and code for De Salazar et al. 2020
      R
      •2•7•0•0•Updated Mar 15, 2023Mar 15, 2023

    • CoV-seasonality

      Public
      Code for regression model from Kissler, Tedijanto et al. 2020.
      R
      •6•8•0•0•Updated Mar 15, 2023Mar 15, 2023

    • disty

      Public
      Disty McMatrixface - compute a distance matrix from a core genome alignment file
      C++
      •
      MIT License
      •1•13•7•0•Updated Mar 15, 2023Mar 15, 2023

    • pr_mort_official

      Public
      Data and pipeline for Mortality in Puerto Rico after Hurricane Maria
      puerto-ricohurricane-mariamortality-estimation
      HTML
      •
      MIT License
      •20•36•1•0•Updated Mar 15, 2023Mar 15, 2023

    • rase-db-ngonorrhoeae-gisp

      Public
      Makefile
      •
      MIT License
      •1•2•0•0•Updated Mar 15, 2023Mar 15, 2023

    • Predicting_Pneumo_postPCV13

      Public
      MIT License
      •0•0•0•0•Updated Feb 22, 2023Feb 22, 2023

    • NM-mpox-reanalysis

      Public
      Files for reanalysis of mpox observational study Wolff Sagy, Y., Zucker, R., Hammerman, A. et al. Real-world effectiveness of a single dose of mpox vaccine in males. Nat Med (2023). https://doi-org.ezp-prod1.hul.harvard.edu/10.1038/s41591-023-02229-3
      R
      •0•0•0•0•Updated Feb 19, 2023Feb 19, 2023

    • rase-db-skeleton

      Public
      Makefile
      •
      MIT License
      •5•2•4•0•Updated Sep 2, 2022Sep 2, 2022

    • rase

      Public
      The core RASE package
      Python
      •
      MIT License
      •2•5•14•1•Updated Aug 17, 2022Aug 17, 2022

    • microbiome_abx_probio

      Public
      Code accompanying Niehus et al. 2021
      MIT License
      •0•0•0•0•Updated Jan 19, 2021Jan 19, 2021

    • africa_export

      Public
      Code for Menkir et al. 2020
      R
      •
      MIT License
      •0•0•0•0•Updated Nov 10, 2020Nov 10, 2020

    • Projects

      Public
      metadata for ongoing or published projects
      Perl
      •1•1•0•0•Updated Aug 16, 2020Aug 16, 2020

    • covid-ma-cases

      Public
      Workflow to pull, convert, clean and categorize data from the official website with COVID-19 cases in Massachusetts
      HTML
      •
      MIT License
      •0•2•0•0•Updated Apr 20, 2020Apr 20, 2020

    • npi

      Public
      Modeling non-pharmaceutical interventions to curb the SARS-CoV-2 pandemic
      Mathematica
      •0•0•0•0•Updated Mar 23, 2020Mar 23, 2020

    • postpandemic

      Public
      SARS-CoV-2 post-pandemic dynamics
      Mathematica
      •0•2•0•0•Updated Mar 23, 2020Mar 23, 2020

    • COVID-19-wuhan-guangzhou-data

      Public
      Raw data used for the Wuhan/Guangzhou comparison with US ICU beds
      MIT License
      •0•3•0•0•Updated Mar 11, 2020Mar 11, 2020

    • detect_prob_corona2019

      Public
      Online code for Niehus et al 2020
      R
      •0•4•1•0•Updated Mar 10, 2020Mar 10, 2020

    • COVID19-scenarios

      Public
      R
      •
      Apache License 2.0
      •3•2•0•0•Updated Feb 25, 2020Feb 25, 2020

    • rase-supplement

      Public
      Supplementary repository for Rapid inference of antibiotic resistance and susceptibility by genomic neighbor typing
      R
      •
      MIT License
      •1•1•0•0•Updated Jan 2, 2020Jan 2, 2020

    • rase-db-spneumoniae-sparc

      Public
      Makefile
      •
      MIT License
      •3•4•0•0•Updated Dec 16, 2019Dec 16, 2019

    • Cholera-Mozambique

      Public
      Modeling Cholera Risk for the Aftermath of Cyclone Kenneth and Cyclone Idai in Mozambique
      R
      •0•2•0•0•Updated May 7, 2019May 7, 2019

    • within-host-diversity

      Public
      Python
      •
      MIT License
      •0•5•0•0•Updated Aug 29, 2018Aug 29, 2018

    • pneumo-data

      Public
      Shell
      •
      MIT License
      •1•2•0•0•Updated Dec 29, 2017Dec 29, 2017

    • samsift

      Public
      SAMsift – advanced filtering and tagging of SAM/BAM alignments using Python expressions.
      Python
      •
      MIT License
      •2•0•0•0•Updated Sep 2, 2017Sep 2, 2017

    • NanoSim-H

      Public
      Simulation of Oxford Nanopore reads. A fork of NanoSim.
      Python
      •
      Other
      •6•0•0•0•Updated May 16, 2017May 16, 2017