Center for Communicable Disease Dynamics – Harvard University's repositories
pr_mort_official
Data and pipeline for Mortality in Puerto Rico after Hurricane Maria
CoV-seasonality
Code for regression model from Kissler, Tedijanto et al. 2020.
cov19flightimport
Data and code for De Salazar et al. 2020
rase-pipeline
RASE pipeline for inferring antibiotic resistance and susceptibility using genomic neighbor typing.
detect_prob_corona2019
Online code for Niehus et al 2020
COVID-19-wuhan-guangzhou-data
Raw data used for the Wuhan/Guangzhou comparison with US ICU beds
Cholera-Mozambique
Modeling Cholera Risk for the Aftermath of Cyclone Kenneth and Cyclone Idai in Mozambique
covid-ma-cases
Workflow to pull, convert, clean and categorize data from the official website with COVID-19 cases in Massachusetts
postpandemic
SARS-CoV-2 post-pandemic dynamics
rase-supplement
Supplementary repository for Rapid inference of antibiotic resistance and susceptibility by genomic neighbor typing
africa_export
Code for Menkir et al. 2020
microbiome_abx_probio
Code accompanying Niehus et al. 2021
NanoSim-H
Simulation of Oxford Nanopore reads. A fork of NanoSim.
NM-mpox-reanalysis
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
npi
Modeling non-pharmaceutical interventions to curb the SARS-CoV-2 pandemic
samsift
SAMsift – advanced filtering and tagging of SAM/BAM alignments using Python expressions.