epidemiology

There are 68 repositories under epidemiology topic.

• WorldHealthOrganization / app

  COVID-19 App

  flutterdartfirebaseappengine-javaepidemiologycovid-19coronavirus
  Language:Dart 2125
• awesome-coronavirus

  soroushchehresa / awesome-coronavirus

  🦠 Huge collection of useful projects and resources for COVID-19 (2019 novel Coronavirus)

  2019-ncov2019ncovawesomeawesome-coronaawesome-coronavirusawesome-listcoronacoronaviruscoronavirus-infocovid-19covid19covid19-dataepidemiologysars-cov-2
  Language:TypeScript 1569
• seirsplus

  ryansmcgee / seirsplus

  Models of SEIRS epidemic dynamics with extensions, including network-structured populations, testing, contact tracing, and social distancing.

  coronaviruscovidcovid-19epidemic-modelepidemic-simulationsepidemicsepidemiologyepidemiology-analysissars-cov-2
  Language:Python 674

• DataForScience / Epidemiology101

  Epidemic Modeling for Everyone

  blogcovid-19epidemiologymediummodelingpython
  Language:Jupyter Notebook 289

• InstituteforDiseaseModeling / covasim

  COVID-19 Agent-based Simulator (Covasim): a model for exploring coronavirus dynamics and interventions

  covid-19agent-basedabmsimulationmodelcoronavirusnpicontact-tracingstochasticepidemiologycovid
  Language:Python 274
• EpiModel

  EpiModel / EpiModel

  Mathematical Modeling of Infectious Disease Dynamics

  epidemicsagent-based-modelingnetwork-graphepidemiologyinfectious-diseases
  Language:R 259

• COVID-19-electronic-health-system / Corona-tracker

  An easy-to-use PWA to monitor the user's wellness and learn about COVID-19.

  symptomscoronaviruscovid-19coronavirus-trackingreactblockchainblockstackdecentralized-applicationshealthpandemicpandemic-disease-trackerpublic-healthpatient-monitoringdiseaseepidemiology
  Language:JavaScript 234

• CodeForPhilly / chime

  COVID-19 Hospital Impact Model for Epidemics

  code-for-phillyepidemiologyepidemicspenncovid-19code-for-america
  Language:Python 211

• CSSEGISandData / COVID-19_Unified-Dataset

  Unified COVID-19 Dataset

  covid-19sars-cov-2coronaviruspandemicinfectious-diseasesglobal-healthepidemiologyhydrometeorologymachine-learning
  Language:R 185
• Python-for-Epidemiologists

  pzivich / Python-for-Epidemiologists

  Tutorial in Python targeted at Epidemiologists. Will discuss the basics of analysis in Python 3

  causal-inferenceepidemiologypythontutorial
  Language:Jupyter Notebook 172
• zEpid

  pzivich / zEpid

  Epidemiology analysis package

  epidemiologyinverse-probability-weightsrisk-ratioepidemiology-analysisrisk-differenceg-formulaipwaipwg-computationtmletargeted-maximum-likelihoodincidence-rate-ratioodds-ratiog-estimationdata-science
  Language:Python 149

• Circuitscape / Circuitscape.jl

  Algorithms from circuit theory to predict connectivity in heterogeneous landscapes

  landscape-ecologyjulia-languagesparse-linear-systemsanimal-movementlandscape-geneticsmovement-ecologyepidemiologyforest-fireclimate-changecircuit-analysisjulia
  Language:Julia 138

• lindbrook / cholera

  R Package for Analyzing John Snow's 1854 Cholera Map

  rcholerajohn-snowpublic-healthepidemiologydata-visualizationdatasetsvoronoitriangulation-delaunayvoronoi-polygons
  Language:R 136

• dreji18 / Bio-Epidemiology-NER

  Recognize bio-medical entities from a text corpus

  biomedicalepidemiologynernlptransformers
  Language:Python 127

• BioDynaMo / biodynamo

  BioDynaMo is a high-performance and modular, agent-based simulation platform.

  simulationhigh-performanceneurosciencemodular-designagent-basedagent-based-modellingagent-based-frameworkbiologyepidemiologycancerlarge-scaleparallel
  Language:C++ 120
• covid19-sir

  lisphilar / covid19-sir

  CovsirPhy: Python library for COVID-19 analysis with phase-dependent SIR-derived ODE models.

  covid19epidemiologypythoncovidcovid-19coronavirusepidemic-simulationsepidemic-modeldata-scienceanalysispython-librarysir-modelbig-datamachine-learning
  Language:Python 112

• wxwx1993 / PM_COVID

  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."

  air-pollutioncovid-19epidemiologymortality
  Language:R 105

• EMOD-Hub / EMOD

  Source files for building the IDM EMOD disease transmission model.

  epidemiologyhivmalariamodelingstochasticidm
  Language:C 103

• IFRCGo / cbs

  Red Cross: Community-Based Surveillance

  non-profitcommunity-projecthealth-informaticsredcrossepidemiologysurveillance
  Language:C# 103
• AMR

  msberends / AMR

  Functions to simplify and standardise antimicrobial resistance (AMR) data analysis and to work with microbial and antimicrobial properties by using evidence-based methods, as described in https://doi.org/10.18637/jss.v104.i03.

  rmicrobiologyepidemiologyantimicrobial-dataamrsoftware
  Language:R 103

• thoughtworks / epirust

  An agent-based epidemiology simulation framework built in Rust

  agent-based-modelingagent-based-simulationepidemiologyrust
  Language:Rust 103
• MicrobeTrace

  CDCgov / MicrobeTrace

  The Visualization Multitool for Molecular Epidemiology and Bioinformatics

  bioinformaticsepidemiologynetwork-visualizationhivcdcpathogensphylogeneticsphylogenetic-treesphylogenyphylogenomicsgenomicsgenomics-visualizationgenomic-data-analysissequence-alignmentnchhstpnchhstp-dhp
  Language:TypeScript 95

• jisungk / RIDDLE

  Race and ethnicity Imputation from Disease history with Deep LEarning

  bioinformaticsbiologycomputational-biologydeep-learningepidemiologyimputationmachine-learningneural-networks
  Language:Python 90

• AlgebraicJulia / AlgebraicPetri.jl

  Build Petri net models compositionally

  chemistryepidemiologymathpetri
  Language:Julia 88
• COVID-19-data

  starschema / COVID-19-data

  Unpivoted and cleaned data sets on the COVID-19 pandemic

  covid-19coronavirusepidemiologyvirologypublichealth
  Language:Jupyter Notebook 84

• ConnorDonegan / geostan

  Bayesian spatial analysis

  bayesianbayesian-inferencebayesian-statisticsepidemiologymodelingpublic-healthrr-packagerspatialrstatsspatialstan
  Language:R 80

• broadinstitute / pyro-cov

  Pyro models of SARS-CoV-2 variants

  sars-cov-2geneticsepidemiology
  Language:Jupyter Notebook 77

• covid19-model / simulator

  Spatiotemporal epidemic model introduced in the context of COVID-19, ACM TSAS, 2022

  epidemicscovid-19infection-hotspotshotspotsepidemiologycoronaviruscoronavirus-analysispoints-of-interestsuperspreaderssuperspreading-eventspoint-process
  Language:Python 75

• elizavetasemenova / prob-epi

  Course materials of "Bayesian Modelling and Probabilistic Programming with Numpyro, and Deep Generative Surrogates for Epidemiology"

  bayesian-inferencedeep-generative-modellingepidemiologyprobabilistic-programmingsurrogatesdisease-transmissiongaussian-processesspatial-statisticsagent-based-modelingnumpyro
  Language:Jupyter Notebook 70

• simonrharris / SKA

  Split Kmer Analysis

  bacterial-genomesepidemiologygenomics
  Language:C++ 65

• epinowcast / epinowcast

  Tools to enable flexible and efficient hierarchical nowcasting of epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes.

  cmdstanreffective-reproduction-number-estimationepidemiologyinfectious-disease-surveillancenowcastingoutbreak-analysispandemic-preparednessreal-time-infectious-disease-modellingstan
  Language:R 62
• spatiotemporal_datasets

  benedekrozemberczki / spatiotemporal_datasets

  Spatiotemporal datasets collected for network science, deep learning and general machine learning research.

  analyticsbenchmarkdata-sciencedatasetdeep-learningdeepwalkepidemiologygcngnnmachine-learningnode2vecpytorchpytorch-geometricspatial-analysisspatial-dataspatial-data-analysistime-seriestime-series-analysisvector-autoregression
  60

• GenSpectrum / cov-spectrum-website

  A web platform to detect and analyze variants of SARS-CoV-2

  cov-spectrumcovid-19epidemiologygenomicsresearchsars-cov-2
  Language:TypeScript 60

• seandavi / sars2pack

  An R package with over 50 highly cited, read-to-use, up-to-date COVID-19 pandemic data resources

  biomedical-datacoronaviruscoronavirus-trackingcovid-19data-sciencedata-visualizationdatasciencedatasetsepidemicsepidemiologygeospatialpublic-healthrstatsrstats-package
  Language:R 59

• tirthajyoti / Covid-19-analysis

  Analysis with Covid-19 data

  data-sciencecovid-19coronavirusanalyticspythonvisualizationepidemiologynumpymodelingobject-oriented-programmingmachine-learningpandemiccovid19-datacovid-data
  Language:Jupyter Notebook 59

• ImpulsoGov / farolcovid

  🚦🏥. 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

  covid-19data-sciencedatastreamlitepidemiologysocial-goodstatisticshacktoberfest
  Language:Jupyter Notebook 55