Disease outbreak reconstruction from epidemiological and genetic data
☆35Mar 24, 2026Updated this week
Alternatives and similar repositories for outbreaker2
Users that are interested in outbreaker2 are comparing it to the libraries listed below. We may earn a commission when you buy through links labeled 'Ad' on this page.
Sorting:
- Reconstruction of transmission trees using genomic data☆72Sep 27, 2023Updated 2 years ago
- Handling, Visualisation and Analysis of Epidemiological Contacts☆17Apr 17, 2025Updated 11 months ago
- Small Helpers and Tricks for Epidemics Analysis☆11Sep 20, 2023Updated 2 years ago
- Simulate infectious disease transmission with contact tracing☆17Mar 23, 2026Updated last week
- Optimised estimates of reproduction numbers over time, which extract more information from an incidence curve than many conventional appr…☆22Dec 9, 2023Updated 2 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- Whole genome core alignments from multiple draft genomes☆13Sep 14, 2016Updated 9 years ago
- Convert dates to arbitrary week definitions☆17Oct 6, 2022Updated 3 years ago
- Long read metagenomics practical at EBAME18☆18Oct 3, 2018Updated 7 years ago
- Create Contact Matrices from Population Data☆21Feb 24, 2026Updated last month
- Flu Scenario Modeling Hub☆12Apr 22, 2025Updated 11 months ago
- ☣ Risk assessment of travel-related disease spread☆19Mar 9, 2026Updated 3 weeks ago
- ECDC in collaboration with Epiconcept developed an R package for monitoring infectious disease surveillance data☆19Jul 24, 2025Updated 8 months ago
- Bayesian inference of ancestral dates on bacterial phylogenetic trees☆97Dec 9, 2025Updated 3 months ago
- An R package to import, clean, and store case data☆25Dec 9, 2022Updated 3 years ago
- 1-Click AI Models by DigitalOcean Gradient • AdDeploy popular AI models on DigitalOcean Gradient GPU virtual machines with just a single click and start building anything your business needs.
- ☆18Mar 20, 2026Updated last week
- [work-in-progress] Curated list of HFOSS (Humanitarian Free and Open Source Software) who are very welcome to external developers contrib…☆13Mar 8, 2026Updated 3 weeks ago
- ☆10Sep 30, 2025Updated 5 months ago
- Analysis of COVID-19 transmission using cluster size distribution☆11Jun 14, 2022Updated 3 years ago
- baltic - adaptable lightweight tree import code for molecular phylogeny manipulation, analysis and visualisation. This fork will no longe…☆12Dec 18, 2019Updated 6 years ago
- Download all EpiCoV sequcnes from GISAID☆32Jun 21, 2022Updated 3 years ago
- Predict MLST directly from uncorrected long reads☆27Oct 31, 2025Updated 4 months ago
- COVID-19 ILI forecasting for the U.S.☆16May 20, 2020Updated 5 years ago
- Bayesian Modelling in Epidemiology Case Line Lists☆14Oct 7, 2025Updated 5 months ago
- Open source password manager - Proton Pass • AdSecurely store, share, and autofill your credentials with Proton Pass, the end-to-end encrypted password manager trusted by millions.
- A {crew} launcher plugin for AWS Batch☆18Jan 5, 2026Updated 2 months ago
- US RSV Forecast Hub☆12Mar 20, 2026Updated last week
- Pipeline to generate NGS reads from a phylogeny☆39Sep 13, 2022Updated 3 years ago
- Analysis of global migration patterns of seasonal influenza viruses☆22Jul 24, 2019Updated 6 years ago
- R Package of methods and data for spatial epidemiology☆34Feb 22, 2023Updated 3 years ago
- Monte-Carlo State Space Models☆19Jul 1, 2024Updated last year
- R app for daily Covid-19 Re estimates☆18Oct 12, 2022Updated 3 years ago
- ☆44Aug 19, 2025Updated 7 months ago
- Code for "A decision algorithm to promote outpatient antimicrobial stewardship for uncomplicated urinary tract infection"☆11Jun 27, 2021Updated 4 years ago
- GPU virtual machines on DigitalOcean Gradient AI • AdGet to production fast with high-performance AMD and NVIDIA GPUs you can spin up in seconds. The definition of operational simplicity.
- Stochastic epidemiological branching simulation☆10Dec 14, 2020Updated 5 years ago
- R package implementing a simple method for CD8 T cell epitope prediction by MHC class I binding for HLA and other MHC-I molecules.☆15Sep 21, 2020Updated 5 years ago
- PhyDyn: Epidemiological modelling in BEAST☆21Dec 22, 2022Updated 3 years ago
- Use a nested folder structure in your package.☆17May 9, 2025Updated 10 months ago
- GraphSNP: Using graph approach to investigate outbreak cluster and transmission in a web browser☆12Oct 5, 2025Updated 5 months ago
- R package for estimation and monitoring of the effective reproduction number in a pathogen outbreak/epidemic☆11Sep 10, 2024Updated last year
- Code for the talk "Approximate Bayesian inference for latent Gaussian models in Stan"☆13May 18, 2022Updated 3 years ago