Center for Communicable Disease Dynamics – Harvard University

Center for Communicable Disease Dynamics at the Harvard T.H. Chan School of Public Health

Boston, MA

Pinned Repositories

CoV-seasonality
Code for regression model from Kissler, Tedijanto et al. 2020.
Language:R86
cov19flightimport
Data and code for De Salazar et al. 2020
Language:R72
COVID-19-wuhan-guangzhou-data
Raw data used for the Wuhan/Guangzhou comparison with US ICU beds
3 2 00
detect_prob_corona2019
Online code for Niehus et al 2020
Language:R40
disty
Disty McMatrixface - compute a distance matrix from a core genome alignment file
Language:C++13 2 101
pr_mort_official
Data and pipeline for Mortality in Puerto Rico after Hurricane Maria
Language:HTML36 12 820
rase
The core RASE package
Language:Python52
rase-db-spneumoniae-sparc
Language:Makefile33
rase-pipeline
RASE pipeline for inferring antibiotic resistance and susceptibility using genomic neighbor typing.
Language:Python6 3 91
within-host-diversity
Language:Python5 3 00

Center for Communicable Disease Dynamics – Harvard University's Repositories

c2-d2/pr_mort_official
Data and pipeline for Mortality in Puerto Rico after Hurricane Maria
Language:HTML36 12 820
c2-d2/disty
Disty McMatrixface - compute a distance matrix from a core genome alignment file
Language:C++13 2 101
c2-d2/CoV-seasonality
Code for regression model from Kissler, Tedijanto et al. 2020.
Language:R86
c2-d2/cov19flightimport
Data and code for De Salazar et al. 2020
Language:R72
c2-d2/rase-pipeline
RASE pipeline for inferring antibiotic resistance and susceptibility using genomic neighbor typing.
Language:Python6 3 91
c2-d2/rase
The core RASE package
Language:Python52
c2-d2/within-host-diversity
Language:Python5 3 00
c2-d2/detect_prob_corona2019
Online code for Niehus et al 2020
Language:R40
c2-d2/COVID-19-wuhan-guangzhou-data
Raw data used for the Wuhan/Guangzhou comparison with US ICU beds
3 2 00
c2-d2/rase-db-spneumoniae-sparc
Language:Makefile33
c2-d2/Cholera-Mozambique
Modeling Cholera Risk for the Aftermath of Cyclone Kenneth and Cyclone Idai in Mozambique
Language:R20
c2-d2/covid-ma-cases
Workflow to pull, convert, clean and categorize data from the official website with COVID-19 cases in Massachusetts
Language:HTML2
c2-d2/COVID19-scenarios
Language:R2 4 13
c2-d2/pneumo-data
Language:Shell2 2 01
c2-d2/postpandemic
SARS-CoV-2 post-pandemic dynamics
Language:Mathematica2 1 0
c2-d2/rase-db-ngonorrhoeae-gisp
Language:Makefile21
c2-d2/rase-db-skeleton
Language:Makefile2 2 65
c2-d2/Projects
metadata for ongoing or published projects
Language:Perl11
c2-d2/rase-supplement
Supplementary repository for Rapid inference of antibiotic resistance and susceptibility by genomic neighbor typing
Language:R1 2 01
c2-d2/africa_export
Code for Menkir et al. 2020
Language:R0 5 00
c2-d2/FungalPathogens
c2-d2/LAC_testing
Language:R1 0
c2-d2/microbiome_abx_probio
Code accompanying Niehus et al. 2021
c2-d2/NanoSim-H
Simulation of Oxford Nanopore reads. A fork of NanoSim.
Language:Python
c2-d2/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
Language:R
c2-d2/npi
Modeling non-pharmaceutical interventions to curb the SARS-CoV-2 pandemic
Language:Mathematica
c2-d2/Predicting_Pneumo_postPCV13
c2-d2/samsift
SAMsift – advanced filtering and tagging of SAM/BAM alignments using Python expressions.
Language:Python