74 Open Source Epidemiology Software Projects
Free and open source epidemiology code projects including engines, APIs, generators, and tools.
Awesome Coronavirus 1466 ⭐
🦠 Huge collection of useful projects and resources for COVID-19 (2019 novel Coronavirus)
Seirsplus 576 ⭐
Models of SEIRS epidemic dynamics with extensions, including network-structured populations, testing, contact tracing, and social distancing.
Covid 19 Electronic Health System Corona Tracker 236 ⭐
An easy-to-use PWA to monitor the user's wellness and learn about COVID-19.
Pm_covid 96 ⭐
Public Available Code and Data to Reproduce Analyses in "Air pollution and COVID-19 mortality in the United States: Strengths and limitations of an ecological regression analysis."
Python For Epidemiologists 104 ⭐
Tutorial in Python targeted at Epidemiologists. Will discuss the basics of analysis in Python 3
Sars2pack 55 ⭐
An R package with over 50 highly cited, read-to-use, up-to-date COVID-19 pandemic data resources
Farolcovid 46 ⭐
🚦🏥. Ferramenta de monitoramento do risco de colapso no sistema de saúde em municípios brasileiros com a Covid-19 • Monitoring tool & simulation of the risk of collapse in Brazilian municipalities' health system due to Covid-19
Circuitscape.jl 93 ⭐
Algorithms from circuit theory to predict connectivity in heterogeneous landscapes
Epitator 38 ⭐
EpiTator annotates epidemiological information in text documents. It is the natural language processing framework that powers GRITS and EIDR Connect.
Chronological Map Phenotypes 29 ⭐
Machine-readable version of electronic health record phenotypes for Kuan V. and Denaxas S. et al.
Covid19 Analytics 22 ⭐
Analysis of the COVID19 outbreak in Brazil mainly through epidemic and hospitalization models, by the Health Analytics and Prospera consulting business units of Funcional Heatlh Tech.
Covid Agent Based Model 30 ⭐
Disease propagation ABM generating SIR, severe cases, and R0 over quasi-time.
Mtbseq_source 25 ⭐
MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.
Lisphilar Covid19 Sir 76 ⭐
CovsirPhy: Python library for COVID-19 analysis with phase-dependent SIR-derived ODE models.
Covid19 Webinar 13 ⭐
A Tutorial on Modelling Number of Infected Cases in Turkey of COVID-19 Using Machine Learning & AI
Globaldothealth List 28 ⭐
Repository for Global.health: a data science initiative to enable rapid sharing of trusted and open public health data to advance the response to infectious diseases.
Covid19_npi_china 12 ⭐
Code for: The effect of human mobility and control measures on the COVID-19 epidemic in China
Msberends Amr 36 ⭐
A free, open-source and independent R package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods.
Covasim 167 ⭐
COVID-19 Agent-based Simulator (Covasim): a model for exploring coronavirus dynamics and interventions
Covid19 Model Simulator 68 ⭐
Code base for the epidemiological model introduced in the context of COVID-19
Spatiotemporal_datasets 32 ⭐
Spatiotemporal datasets collected for network science, deep learning and general machine learning research.
Taiwan Covid 19 2021 27 ⭐
Data, methods, and results of analyses tracking the May 2021 COVID-19 outbreak in Taiwan.
June 21 ⭐
June is a framework for agent based modelling in an epidemiological and geographical context.
Trackingr 19 ⭐
Python code for "Tracking R of COVID-19 A New Real-Time Estimation Using the Kalman Filter".
Bc Covid Epi Rt 12 ⭐
A method to estimate Effective Reproductive Number (Rt) using the province of BC's case report data.
National_causal 12 ⭐
Public Available Code to Conduct Analyses in "Evaluating the Impact of Long-term Exposure to Fine Particulate Matter on Mortality Among the Elderly."
P J R Covid 19 11 ⭐
Stochastic SIR models; adding age-structures and social contact data for the spread of covid-19. Lattice model for identifying and isolating hotspots. This has been further developed into a network(graph) of multiple clusters(lattices) and tracing the infection in such a population.